All I'm really suggesting is heavier ammo limitations. 70 CDs vs the 20-50 missiles a cap can load into a turret, along with additional counters like CMs and flaks, render those ordnance weapons pointless, and that's just from one fighter/bomber/gunboat/cruiser/battlecruiser focusing on destroying incoming missiles and torpedoes. IMO flaks should probably have ammo limitations as well, and countermeasures likewise tend to have too much 'ammo' (though at least they arent 100% effective).
Destroying ordnance in the manner I'm implying doesnt require explosive radius, so no, there's no deterrence to using train/reinforced CMs. All you have to do is target the torpedo and fire a disruptor, and the end result is 100% effective.