And it's good to have spare ECM or shield system, or weapon in hold... just for case. If something will happen to your own and repair bot cannot can fix it, maybe it could be replaced.
As a side note, salvage is not the same as cargo neatly packed in containers and accurately delivered up to shock mounting in hold. It was beaten and shaken, and a bit burned on that corner.
1.1) re-mounting missiles to pylons is a good option. As long as it requires turning jets off (maybe, dropping shields as well) and waiting a bit, it cannot be done in combat anyway, and it requires bot to perform trick, but it would be handy anyway...
More along FFE line:
2) Guns consumes ammo while shooting. Reactor consumes fuel while it generates energy.
Both have their own reserves but can be reloaded from hold (theoretically). Why not to use some way to generalize this ? Then more can be done with the same tool. E.g.: sublimative cooling expends water. Repair and lifesupport perhaps need Fuel_Cell. Rlaan version needs CCBB plus BioApplicator and BioRemodeler for repair.

2.1) Install automatic feed system for each gun and launcher and reload on the fly. Yes, like in real military ship, and for each of turrets too. But this will be major ship modification, not something which can be plugged in or out. So it's not removable (but still can be damaged), takes considerable volume in hull and price is steep.
3) device can have assigned cargo types. Then repair bots must expend certain cargo to repair specific systems, Hull_Patches for hull and appropriate alloy to repair armor. The same may appear as a salvage when unit or subunit is destroyed. Docks require aerospace equipment, lifesupport needs Atmospheric_Scrubbers, repair system needs Assembly_Tools and Welding_Lasers. If it can reanimate capship in sensible time it probably requires Robot_Workers too. Nuclear_Pods or Fusion_Injectors for reactors, computers for turrets and radar, AI_Cores for repair AI. Lasers may need certain gases. Throw in handful of gears, metals and suchlike, and in-flight repair is not easy and free anymore, though still faster and easier than on alien base.