You can drop an unboiled chicken egg to no ill effect from a 4 story building if it's inside a cardboard box suspended in pantyhose.
Bad enough things happen in Earth labs that they can have, or should have independent lifesupport. On an alien ship however that life support might include independent structural integrity fields and inertial dampeners... How do spaceships work in this fiction? Did they use hyperspace, warp realspace or use relativistic speed.
The trip took 5000 years.
Even if relativistically the trip took a month from their perspective, they'd still use suspended animation rather than figure out how to carry additional food and water for millions of people for one month.
Did any one stay awake for portions of the trip if it did take 5000 years flat?