Had a thought, and sorry for derailing the thread from super amazing models in-engine to destructible capships.
Alien capships had this shield emitter mechanic, where components would be undestroyable until the emitter is destroyed. The component would be labelled in blue, instead of the damage-dependent green/yellow/red. What if, we repurpose that in some way? We make a "hull" component, targetable as a subtarget, but blue/invincible? Pretty sure AI bombers won't even try to torpedo blue components, so you won't have wingmen wasting missiles on an undestroyable object. Make it so the capship itself doesn't have a basic mesh. Instead the component takes up the rest of the capship model and has two versions, hull and hulld (destroyed). You'll never be able to destroy the hull yourself, but when the bridge/engines are destroyed and the capship self-destructs (remaining turrets, hangars, launchers, plasma weapons, blow up when both bridge/engine(s) are destroyed), the hull switches from "hull" to "hulld". The only problem is, you'll be able to target the hull as a sub-target of the capship. Unless you can make components unselectable, which I don't think you can.