A thought:
You first roll a d6 and if its a 6 you then roll on the d66 table. If that roll is 11-19 (i assume its supposed to be 11-16) nothing happens.

In that case we have two rolls ending in nothing. I would suggest that whenever a roll is made on the table, SOMETHING will happen. Rolling several times resulting in nothing is kind of boring!

The 11-19(16) result should be included in the first roll. If you feel 1/6 chance of an encounter is too high (which i think it is) then change it to rolling 2d6 and a result of 12 (adjusting down to 11-12 or even 10-12 if you fancy more encounters) means you roll on the table.

A thought:
You first roll a d6 and if its a 6 you then roll on the d66 table. If that roll is 11-19 (i assume its supposed to be 11-16) nothing happens.

In that case we have two rolls ending in nothing. I would suggest that whenever a roll is made on the table, SOMETHING will happen. Rolling several times resulting in nothing is kind of boring!

The 11-19(16) result should be included in the first roll. If you feel 1/6 chance of an encounter is too high (which i think it is) then change it to rolling 2d6 and a result of 12 (adjusting down to 11-12 or even 10-12 if you fancy more encounters) means you roll on the table.

That's actually a good point, having a 5 in 6 chance of nothing happening, then a further chance of something still not happening seems compacted redundancy. Still a great table though and I do plan to pluck from it.

Good points! I don't know if it's really impact things, but instead of "nothing happens" as the text, it could be "false alarm" or something like that, which could prompt the GM to consider if it was truly a false alarm or if it's something else. Regardless, I'm glad the general premise of the table seems to jive with people.

False alarm is quite a good idea.

Since there was interest in this idea and a lot of useful feedback, I've attempted another draft of my idea. I'll note the general changes and things of note at the bottom, and let me know what you think!

Once every 10 light years (or about 3 parsecs), roll 1d6. If the result is a 6, roll the table below:
d66 -- Space Travel Encounters

• 11-16: False alarm Or so the ship’s computer says at least…
• 21-23: Intermission The ship’s computer brings the ship out of hyperspace early, and then wakes the crew. What’s the story?
• 23-26: Wreckage A small piece of wreckage is spotted on the sensor scope; a cargo container, escape pod, frozen corpse, part of a starship smashed or blown off, etc.
• 31-32: Encounter Despite all odds, an unidentified object is detected by chance along their path. If the PCs investigate, roll tables on page 352 - unless it’s something stranger...
• 33-34: Turbulence An unexpected ion storm falls upon the PC's ship. Roll for a minor ship complication [page 198-199]
• 35-36: Drifted An unforeseen course correction is needed to reach their destination - add 1d6 light-years to the travel needed, with potential pay deductions pending. If profit can be found elsewhere though...
• 41-42: Lost The ship’s computer stops as it's navigation system has lost its bearings. Add 1 unpaid week to correct.
• 43-44: Military A military starship orders the ship to stop so they can send over a small search party for a “routine” ICC and customs check. Should the PCs be worried?
• 45-46: Disputed Territory The lines of claimed space have shifted during travel, and the PC's ship is now in disputed territory, potentially in danger of collateral damage from a space battle, or worse...
• 51-52: Blindsided A neutrino burst slams the PC's ship. Roll for a major ship complication [page 199]
• 53-54: Ambushed The PC's ship is tricked into halting FTL travel by a space pirate trap.
• 55-56: Infected An alien fungal infection slipped unnoticed, even in the hypersleep pods, until now. All players gain 1d6 Disease level. [see page 109 for more]
• 61-62: Irradiated The ship crosses paths with a stray gamma ray burst! All players suffer 1d6+4 rads immediately, and the sections of the ship they were in have the weak radiation condition until decontaminated. [see page 110 for more]
• 63-64: Black Hole The PC's ship travels too close to an uncharted black hole. Immediate action is needed to escape the grip of  the event horizon!
• 65-66: Twist The truly unusual and unfortunate happens! Roll for a plot twist [page 350]

Some notes:
1) Since my intent was to provide a chance at a random space encounter the more you traveled in space, not the time you spent in space, I changed the condition for rolling to light-years instead of weeks. The idea is that it should be fairly unlikely if you're traveling within the sort of distances in the core worlds, but likely if you're going to and from, say, Earth to the Frontier, and while the chances of needing to roll are less than before, there's still a chance of potentially rolling for the table many times if trekking from one end of the Middle Heavens to the other. As with anything, the table is first and foremost a means of generating ideas for the GM to allow lengthy travel to be peppered with situations, so they don't need to blindly follow this if it would end up with, say, 2 black holes over a 20 light year journey. With that said, I partially picked the numbers for (hopeful) ease of use as well, but I'm open to other ideas.
2) Changed "Nothing happens" to "False alarm" to give the sense that something /still/ could be the case, or at least make the players uneasy.
3) The order of the table should now be (roughly) listed from least problematic (top) to most problematic (worst).
4) I tried to give each of them one or two keywords at the start, as some of the other official tables do, so that it's obvious what the spirit of that roll entails.
5) I reworded the possible ship/etc. "Encounter" to hopefully emphasis that the ship isn't literally in their way.
6) Similarly, I reworded the "running into a space battle" portion to indicate that the players simply are now in disputed territory, leaving the specifics of what that could mean up to the GM with some potential prompts.
7) Since there's doubt as to whether a ship at FTL can be physically stopped, I reworded the pirate "Ambushed" to imply that there's some tech-trick they can use to tell a ship to stop instead, which should be more believable.
8) For Infected, I noted specifically that it impacts players in hypersleep. I don't actually know what hypersleep could protect players from, but at the very least, this could be treated as them waking up with this.
9) I'm still uncertain if I made the scenario well enough for "Irradiated" -- I want them to have to deal with radiation to a level that matters but not guarantee some sort of total party wipe either. I suppose, like the more official tables, I could have left it more narrative and allow the GM to decide (which I more or less went with before) but since there was confusion, I took a stab at this instead.
10) The numbers for the table should be (hopefully) right now. Most have a 2-number spread, though "False Alarm" has a 6 spread and "Intermission" and "Wreckage" each have a 3 spread.

That's a great table mate, it or something like it will certainly be getting used at my table.

Thanks! I'll be curious how it'll fair in the 'real world' gaming, hah! And of course, if I get a chance to use this, I'll let you all know how it turns out on my end.