Steve, does the AI make any efforts to conserve ammunition or does it keep firing missiles as fast as possible until all targets are destroyed? From your story it sounds like they NPR might have used some intelligence in how it fired missiles. Otherwise I could imagine an AI fleet emptying its racks at a single freighter if the missile flight time was long enough.
They do attempt to conserve ammunition in certain circumstances, as the above freighter annihilation situation was one of my early concerns.
On the thought of "disallowing" building up missile swarms. I also would not like to see missile waypoint targeting eliminated. Perhaps if missiles upon reaching a waypoint were to continue on their last course in a ballistic manner until manually given a new target, that would be a way to reduce gathering them for swarms. Or at least make creating a swarm require a lot more planning and skill.
One of my primary designs goals is to avoid micromanagement. Therefore, I don't want players to have to play around with missile salvos too much on a regular basis, although it would be ok for occasional recon drones, etc..
At the moment I am leaning toward some type of very short range (10,000 km max), very long recharge (at least several hours) weapon or EW system that would attack all missiles about to hit that ship. It would cause perhaps 1 point of damage so it wouldn't be that useful in an anti-ship role and it would be wasted against small salvos. It wouldn't eliminate the massed salvo but it would give the attacker player something else to consider. The idea for this came from the static screens (I think that was the name) in Traveller. This won't be in v4.0 because i need to give it some serious though. I will probably include this when I do the EW overhaul.
Steve