Previous Starmada editions had a few things, especially Starmada X.  There were some issues with it so I could see why it was removed.

One idea that just came to mind is use the Full Thrust system check system for your criticals.  Since the current Starmada SSD has a row of 6 colums for hull (and engines and shields), then when you get to the end of a hull row check for all those systems that normally don't damage through the regular Starmada damage system, namely, everything in the Special box.  S:X had you roll 1d6 for the number of Marines that got killed, you could apply this to Anti-Fighter Batteries as well.  For large SU things, like Science, Cargo, Repair, Transport, you could roll 1d6 and multiply by 10.  Some things probably cannot be damaged, like Armor Plating and Regeneration.

As to repairing them, one way would be to make your regular repair rolls and if a die shows you can repair something that isn't damaged then you could apply that to a Special of your choice (but no resurrecting of Marines, they might be tough but they're not that tough!  ).