This issue happens to most types of ships, not just bombers. Gunships are probably the least likely to get it because of their longer range, which makes it easier for them to find something to hit. I have been marked as inactive and lost 25-30% of my reqs in the following situations, while flying either a scout or strike fighter:
1) In a deathmatch, I was in the middle of a dogfight against a player who was extremely difficult to hit. He was flying evasively, zooming around asteroids, using his distorsion field active ability every time it was off CD, etc... I just couldn't hit him. I was marked as inactive while I was shooting my blasters at him!
I had a match where I scored 75k damage, 15+ kills and 10+ assists... and got docked 22% req for inactivity...flying a tier 1 scout.
I believe it was for exactly what you point out in point 1)
I can barely think of any time during that match I was not hitting something aside from chasing one slippery scout.
Regardless the timer needs to be adjusted for sure. If a tier 1 scout can get penalized that easily while actively dogfighting, its no wonder bombers and slower craft are getting docked 50% plus some games.