Update: I found the place where the actual game files were kept after some digging, and installed the no-cd patch, but the problem persisted. Any ideas?
I'm also having this problem with the Steam version, even after applying the No-CD patch. It is extremely annoying. Torpedoes still seem to do the usual amount of damage, but AA and artillery are almost totally ineffectual. Sometimes if I keep firing long enough it does eventually start to damage the target (this is after a few minutes firing "Super Reload"!) but it makes the game almost unplayable.