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It is said that after the Portal Wars, the Third Horizon was isolated and fell into a major economic downturn and technological regression, and that the Firstcome basically lost their History and became planet bound local cultures with all previous history becoming vague myths and legends. Or something to that effect.

I can't rationalize that at all at the moment. In a world where the info net exists, and databases etc, how can one "lose" their History. Also, how can the Zenith arrive and be the technological leader when it is a 1000 years old? It just makes no sense to me.

Well, it's hard to rationalize not just for you. This topic was brought up many times here on this forum (here, here and here), and outside the forum. As far as I can tell two methods are dominant:
1) It is what it is, don't overthink it.
2) The timeline is hard to believe, so you should extend time of Portal Wars or the Long Night or both.

I and my players are going with the first method, at least for now. It's beacause that historical aspect isn't so important in our game. 
Of course we attempted to rationalize:
We have assumed that twenty-something years of war in galactic scale can be so destructive that databases, info nets etc. were practically destroyed or they outlast in vestigial form. The Long Night is the century of isolation not only from other Horizonts but within Third Horizon too, so it didn't favor reconstruction or development of new ones. These are the times of "famine, plague and despair" (Core Rulebook p. 181). Probably there were more wars, but on planetary/system scale. It makes the decay more plausible. In my games I treat Astrodiarium as databese created by Foundation from parts of the "local" databases, but mostly from Foundation own research, that means from scratches.
Moreover, after reading "History of the Horizon" chapter in "Atlas Compendium", one can imply that the remains of knowledge about other Horizonts were systematically eradicated (of course it can be my overinterpretation).
As for Zenithians, I don't see them as technological leaders, at least not in the moment of Zenith arrival. Their power was that they were more pragmatic, innovative, open for trade, exchange of informations, knowledge. Technological development of Third Horizon since they arrived is not an effect of their superior technology but their actions to reconnect people living in Horizon and to rediscover Horizon. Also, Zenith was 1000 years old but, I suppose that on its board there was some technological advancement all this time - limited by conditions but nevertheless. There were laboratories, workshops etc.

So I'm toying with using paranormal explanations for the current state of things. Maybe a kind of Darkness between the stars induced black out of the mind, that the Firstcome had to fight using the Icons as the last bastion of their identity, religion as a shield against DbtS induced insanity? This Darkness would probably have been unleashed by the First Horizon as a weapon to subjugate, a sequel of the Portal Wars, as such.

Personally I don't like the idea of waeponization of Darkness, but neverthless it's interesting concept. 

 Thanks for the very good input!

Regarding the weaponization of the Darkness, I'm not thinking of using Darkness as a fuel or ammo or whatnot, but more that the FH leaders in particular have gone over to a kind of worshipping of all products of the Darkness and use its powers to nefarious ends, a bit like Emperor Palpatine doen't build Dark side TIE fighters, but uses the Dark side to corrupt powerful individuals, cause fear and generally mine the will to fight of any who oppose him.

P.325 or the core says: In the First Horizon, man- kind has tamed the Dark between the Stars and uses it to create energy and to sculpt life. This practice has in turn warped parts of the First Horizon, especially its rulers.
"In the First Horizon, mankind has tamed the Dark between the Stars and uses it to create energy and to sculpt life. This practice has in turn warped parts of the First Horizon, especially its rulers."

Also, in the Darkbound description:
"Perhaps they have been turned bad by djinn or efrites, been exposed to corrupting dark forces or formed horrible pacts with cadaver clocks or dark cybernetics."
So dark cybernetics do exist, the unholy alliance of tech and Darkness is a thing.

But my main idea is to tie the piousness of FC cultures to the metaplot. What I mean is that during the Portal Wars, the FC will have fought to horrible creatures created by the FH leaders, and will have seen first hand the corruption and evil of the Darkness. From that experience has hatched a fanatic hate or fear of anything that comes close to the Darkness. If you look up the effects of Darkness in the core, as soon as you are in space for a prolonged period of time, you are affected. Portal jumps also affect you.

So I like your idea that localized wars for ressources were happening all the time during the Long Night, but also, the FC basically stopped using the Portals and even avoided space altogether as much as possible. Portals to the FH were destroyed (seen as gateways to Hell, literally), and the Cult of the Icons was developed with a very anti-darkness dogma.

Then the Zenith arrived, and with it the Zenithians, a large community of pragmatic spacefarers that have no fear of the Big Dark. This advantage gave them the possibility of reopening the space routes and to seize the bulk trade market rapidly.

Now the Zenithians have pieced together what happened on the TH, and of the possible existence of an unknown energy, Darkness, and so they have pragmatically started to seek the blessing of the Icons to protect their endeavors. But they remain scientific, sceptical and much less superstitious than the FC, as is canon.

What do you think?

P.325 or the core says: In the First Horizon, man- kind has tamed the Dark between the Stars and uses it to create energy and to sculpt life. This practice has in turn warped parts of the First Horizon, especially its rulers.
"In the First Horizon, mankind has tamed the Dark between the Stars and uses it to create energy and to sculpt life. This practice has in turn warped parts of the First Horizon, especially its rulers."

Thanks for pointing this out. It had completely slipped my mind. In that case I really like your idea about piousness of FC. I am still thinking that it was strong long before Portal Wars, but it's plausible that these events could make it even stronger, and give it new, more "scotophobic", angle.
On a side note I think it's interesting that this piousness is really conected to ritual side of religion and it is opposing its mystical side and mysticism (at least officialy). So we would have First Horizon with Darkness, Second with Symmetry's mysticism, and Third with cult of Icons.

I like the idea that all the societies in the Third Horizon right now are actually fairly new in their current forms. The Portal War was so brutal, so destructive and so all encompassing that when it ended, all the cooperation between the various factions as they were then slowed massively as they desperately tried to save their dying civilizations. Whole planets were depopulated as the lack of interplanetary trade stop. Cities emptied as massive grain shipments from agricultural worlds stopped.
Many worlds were flung into civil war as various factions (small f) fought over dwindling resources. At the same time, doomsday cults strang up, first horizon cultists ran amock and religions struggled to hold people together. Libraries were burned, royalty assassinated, populations poisoned. The purge of information relating to the first horizon was to stop the cultists and fanatics. Huge purges began to cut out these heretical movements. Distrust was rampant. Brutality and authoritarianism were welcomed as the only solution to the chaos.
Eventually civilization returned, built on top of the ruins of the old world. The Factions are the most successful attempts at rebuilding. Some existed before the Portal War but even those have had massive changes forced on them by the near collapse of civilization. Many have a strong philosophy to hold a people together. Something to counter the nihilism of the era.
When the Zenith arrives, they have a massive advantage. They have no history in the Third Horizon. No cultivated distrust. They can act as a middle man and whats more, their whole crew is made up of people who signed up with hope and optimism. They weren't fleeing a dying earth, they were excited explorers and colonists. They WANT to meet strange new people, sell them stuff and settle on strange new worlds.
So suddenly trade exists, facilitated by the Zenithians, and of course as soon as it exists, all the old factions realise they want some of this market. They dust off their old starships, un-mothball their shipyards and get to work.
But so much has been lost. So many colonies, so much knowledge. Sure, that knowledge may exist somewhere, in ancient databases, or religious libraries. But who has access? Who even knows where it is? This also creates a great environment for adventure. You can have firstcome ruins that have laid empty ever since the war becase who even knew they were there? You can have advanced technology from Portal War era warships that has not been used since because the records of it are tucked away in some secret shipyard that was abandoned when the supply shipments stopped.
And the Zenithians don't necessarily have the best tech, but they ALL have access to the same reasonably high standard. Whereas the firstcome have better tech but its secret, hidden, used only by certain groups, etc. So the firstcome don't have anti-matter drives, its only the Order that have them. And the firstcome don't have proxy tech, its only Ahlam's Temple. Whereas theres far less variation in the tech between the zenithians as they all started at the same level not that long ago. Draconites aside obviously, but they are a special case.