Swarm refire rate will be reduced, and about armor upgrades... What ships are affected? Have you tested original ships other than Eagle? If yes and they behave same way, this might mean that armor upgrades are buggy and should be removed from game, I'm afraid. This is a serious issue.
I suppose this is partly related to ship parts thing. Parts of ships, when hit, affect the rest of the ship, and armor upgrade only applies to central part of hull. So when part is hit, all ship gets same damage as if the hull had no armor upgrade. Of course I might be mistaken...