SpaceCat The idea would be simply limiting the number of missiles a launcher module can control - so no further missiles can be launched/controlled until the allready in air missiles are depleted/exploded.
I'm not sure this would affect missile spamming at all. All it would really do is create de-facto missile damage falloff and nerf side-fire missile designs. If the missile cap is based on # of missile launchers, then missile spam really isn't affected at all, just missile range. It would work if missile cap was based on a part other than missile launchers (e.g. sensors or control rooms), but that would probably feel unintuitive.
Walt Auto-firing ion beams would basically be anti-missile walls. (Not necessarily a bad thing, though.)
Could missiles block the ion beam while they're getting destroyed, instead of just evaporating without affecting the beam?
Whatever ends up happening, I think it's important that missiles vs pd have more variables than it does right now. IMO this could be accomplished by drastically, drastically cutting PD arc but hugely increasing PD effectiveness (PD can't cover an entire ship side - Mc2 would like this change because a PD-only ship would be better), by allowing more weapons to target missiles (which would normalize missile damage across ship types), by giving missiles more options to avoid PD (specifically player-controlled guidance), or probably lots of other things. Personally, I like the idea of doing all 3.
Any changes should probably wait for the different missile types update though. Thematically they'll fit better, and there's no point fine-tuning missile balance now only to throw it all out the window with new missiles.