I just wiped out a few enemy ships and lost one of my own in return. My ships each have 200 cryo berths. When I picked up my and their survivors, everyone piled into two of my four remaining ships.
I have 800 cryo berths across the four ships, and am carrying almost 1100 survivors, so definitely I should be (and am) seeing messages that my ships are overburdened. However, I'm only getting messages about the two ships which are packed to the gills; the other two ships are not carrying anyone and hence not seeing accelerated morale decay.
I would like to suggest a change to how pickup of survivors is handled, i. e. to evenly fill up cryo berths across the fleet, then when those are full, evenly distribute the survivors across the ships in the fleet based on ratio of crew berths.
It would also be useful to have a way to do that manually with a fleet command, i. e. if I wanted to have a "prison transport" ship to load everyone onto and send back to my home planet.