All Blue Planet warships - whether GTVA or UEF - were generally conceptualized as both heavily armored and heavily compartmentalized. Crew spaces make up a minority of the ship's volume.
Ships are layered in a sandwich of ablatives, shock dispersal, non-Newtonian fluids, radiation tanks, and old-fashioned physical belts of metals and ceramics. The armor is studded with sensors, integral electronic warfare systems, and conformal shield generators of the type seen on the FreeSpace 1 Stiletto bomb, which propagate through the hull rather than above it.
Damage control to the armor proper is difficult under combat circumstances. UEF warships take one approach - damaged hull areas are sealed with layers of rapidly coagulating polymer coating, like a scab. This can't match the original armor plating but will stop incoming weapons fire to a degree. GTVA ships rely on their integral shield systems to recruit and bind repair fragments. Damage control is rarely conducted at the surface of the ship.
In the future you'll be seeing warships on both sides employing more active countermeasures too.