To clear things up:
Fighter Mode:
Kills Hit Percentage = hits on planes (and most probably ground vehicles as well, as I repeatedly saw my hit % going up after strafing LVts in a Hurri I. Still has to be confirmed)
Attack Mode:
Kills hit percentage: Gun hits on everything: Planes, vehicles, buildings
Damage Hit percentage: Hits on objects (buildings, gun emplacements and so on) with ordnance (bombs, rockets, torpedoes)
do MG hits on objects (like tanks, buildings, etc.) negatively affect accuracy if they don't destroy the target?
No.