Repair bays only fix internals (not armor or shields), and if the repair bay is hit, well it can't repair at all.
In stock, shields only regenerate if the ship/base/etc has a shield regenerator.
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I reccommend trying my P&N-ism Mod (so far, I've reworked the physics in just the first two of the three campaigns).
The usefulness of armor has been beefed up, the weapons are more diverse, shield generators have built-in regen, crew quarters provide more crew and help repair the ship, lifesupport is more detailed, and a bunch of other things too.
Two big points you should know before you start:
- Big ships are tough. Fleets are even tougher. Don't be surprised if you get shot down by a couple of destroyers and have to retreat. Fighting alongside allies is the safest path.
- Lifesupport is Critical. Have 2 or 3 times more than you need, if you can afford it, and spread it out for safety. Crew quarters help here too by drastically increasing your crew count. This works double, by giving you more time before everyone dies, and by speeding up repairs.
Also;
- Power is harder to come by. Grabbing enough reactors to fire continuously is unlikely. Instead, try installing some plasma capacitors. They'll tide you through battle and let you charge up while you cruise around between fights.
- Buyer beware on high-energy discharge weapons. As their name implies, they dish out copious amounts of damage, but will suck your power dry in seconds. A wave-motion gun can burn through 100x what a (5kt) standard reactor can generate.
Energy storage is important here
- Keep an eye out; often it is cheaper to throw out your old armor and buy fresh plating, rather than repairing it.