In this patch, and in patches previous, I place Blast Doors on all combat ships as a rule. It's a head canon thing, like Recovery Shuttles on all carriers with human pilots. I like to imagine it raises morale, increases loyalty, and most importantly, it does actually save lives.
It's unfortunate that most of your fleet was disabled. I lost a wing of frigates carelessly just the other day while I was distracted. Whether or not you're committed to using Blast Doors, I highly recommend having a Nebula (or two) or a Starliner in your fleet with built-in Additional Berthing, depending on your crew requirements. Ideally, if you're expecting heavy casualties, you will need to cover at least 75% of your combat ships' total crew requirements in the space your personnel transports provide. That is to say, you do not need to have that space filled with replacements, just available to host survivors while ships are recovered.
As you are no doubt aware, it is still helpful to have replacements available in case of a mass casualty event. But, do not be tempted to fill your berths to their limit if you are using Blast Doors, or the overflow will be lost.
Good luck on your next engagement, Captain.