I think that PD weapons having really good range is because their projectiles have to be fast to hit small targets like missiles and they aren't blocked by other friendly ships.
The balance is that they usually arent too powerful, and future changes to shields may nerf down the damage.
The problem with PD having insane range is that AI targeting priority can be an issue since they like to shoot at the currently targeted ship.
Anyways irl ships have gotten hit and damaged by CWIS so its still realistic. The rest is just a quirk of fighting in space.
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If the (surface) armour reaches 0 on any part of the ship (maybe when blasted off by high-explosives), I suggest that fragmentation ignore surface armour so that they still have some use even if they can't wreck the stuff further inside.
Anything powerful enough to blast the armor off a ship is powerful enough to blast the ship itself apart.
I recall from the field manual that the surface armour is 1/13 as thick as the citadel armour, and that the compartment is basically a buffer space between the surface armour and the citadel armour. A blast in the compartment should break up the surface armour and contribute to its failure. But that only applies if HE is a blast and not a penetrator.
Fighters end up shrugging off point defense systems, and no hullmod or skills apply to increase damage dealt to fighters or missiles. Is there a conflict somewhere?
Please elaborate: are they absorbing point defense weapon damage?
Some (heavy) fighters and gunships rely on armour, and with certain settings can become immune to point defences. There is no way to configure them separately from ship stats. Because armour does not degrade, if PD cannot damage them, then the target ship is effectively defenseless.
Also, I'm running Archean Order TC which has skills and hullmods buffing PD weapons against fighters by 250%, 200%... but this mod does not apply them.