As Montezuma said, the NPCs are practically idiots with the SNAC. The only time they should conceivably hit you is if you're flying straight at them or are in something bigger than a gunboat.
I will agree, however, that the missions like to spam tons of NPCs. This also isn't much of a problem if you can pull off some fancy flying or have backup. It does get annoying when the NPC gunboats like to randomly spawn.
Maybe some day, they'll see a hero is just a man who knowshe's free.