I am certain that all kills in ships gun or field gun are NOT counted toward score or rank. I also think that kills of GVs when in fighter mode are also not counted (though I could be mistaken about that). IIRC, when you select "fighter" mode at the beginning of a flight only AIR-to-AIR hits and kills count. If you are in "Attack" mode all hits (GV, AIR, Building, structures) count toward points, score, and hit percentages.
As to the "Why?" .... at the risk of sounding like a smartprettythang, because that is the why HTC chose to score the hits. I guess in the grand scheme of things it is to encourage your to plan your sorties and follow your plan to be rewarded. If you up in fighter-mode and shoot ground targets your score is affected (negatively). You have to plan to be a fighter and do just that.... If you always up attack mode and never shoot ground targets, your score is equally affected.
I also think you do not get points / kills for bombing airplanes in bomber mode. In bomber mode your only points come from destroying ground targets -- again, I could be mistaken, but I think this is how the system is setup.
