I agree that teh Nadir was probably sent somewhere else, whether by prime directive or being lost. If it was headed to the Third Horizon, I dont think they would be angry. The would be hardened by their strange voyage and could be better for it, or be twisted and corrupt like the crew in Pandorum.
Although we would like to know what happened to it, its not the focus of the game. Coriolis focuses on Coriolis Station, the re-purposed Zenith, and its influence on the Third Horizon.
But looking at the definition of Nadir, we can speculate a lot
Noun: the lowest point in the fortunes of a person or organization.
"they had reached the nadir of their sufferings"
The Nadir is truly lost and we shall never see it. Its provided as a juxtaposition to the survival tenacity of the Zenith.
Similar: the lowest point, the all-time low, the lowest level, low-water mark, the bottom, as low as one can get, rock-bottom, the depths, zero, the pits
Fate of the Nadir is its travel through literal hell, akin to the Black Hole. Perhaps like I mentioned above they have changed so much they are the darkness between the stars, they are the shadow of everyone else who survived.
Astronomy: the point on the celestial sphere directly below an observer. [/i]
With Coriolis directly above Kua, perhaps the Nadir are the true first come?