I did not really find the weapon variety lacking. Starshatter is not FreeSpace: with the exception of a few different types of aeroplanes throughout history, hardly any could easily rotate in a new type of gun armament on short notice. Warplanes are oft built around their weapons - changing internal armament means that much of the internals must be re-arranged, the center of mass shifts, etc. Starshatter, though the style is a bit more fantastic than realistic, still aims to be more of a realistic sim than an arcade sim like FS.
...I realize your comment is about capship weapons, but even still, ship weapons are relatively limited as well. Once a system is installed, it is not terribly easy to rotate it out. FS tends to field a large variety of systems on short notice, but in reality, that's not terribly feasible and possibly presents a logistical challenge. SS is the opposite, and forces you to deal with the fixed weapons of the vessel. Any weapons refit would involve getting the ship back into "mooring" of sorts, where the vessel could then be serviced.
I have read that shields are there principally to deflect beams. Perhaps particle beams are easier to fend off than bombs in the far future, and that's what you must keep the PDBs around for? For better or worse, starfigher ASMs cannot be shot down, though there is a mod out there that does that, too.
I'm also not sure all of your subsystems can be fully repaired or replaced between mission, though I never enjoyed capship missions. Hence, I'm drifting into territory I do not understand. But, I recall that your engineering window lists only so many spares, etc.
As far as net damage, tell me you will fix this for next mission:
...Which is 8 hours from the last one.
If a gun turret is down, it is possible a new one can be dropped into its mounting. But, if there is extensive hull damage, yeah, you're not going to fix it in a day.