You can take the cryo berths off of the Rescue Shuttle. They are redundant.
That depends how long you intend to deploy the rescue shuttles for. These ones have a deployment time of 6 days, enough time for the overcrowding mechanics on ships to kick it and give a few thousand percent increase in deployment time. I've had this exact issue with my rescue shuttles when I overloaded them, and even years after the mission their deployment counters still haven't hit zero.
The morale penalty for overcrowding won't matter for this ship. It doesn't do anything that depends on morale.
Overcrowding on a small cryo-less shuttle (10 crew vs a much larger number of survivors rescued) will likely cause life support damage at the end of each construction cycle, but that damage is prevented if enough MSP is on hand. The tiny crew quarters only takes 1 MSP. The shuttle carries 50.
The cryo berths are 1/2 of the shuttle size. If you take them off, you can fit four shuttles on the Haven instead of two. That seems like a worthwhile tradeoff for having to pay 1 MSP whenever a shuttle is deployed at the end of a construction cycle.