For the most part, yes. The minor exception being GV, while not counting for kills they still count for hit%. Found that out long ago while having to kill LVT's in the Hurri I.
OK, well that is probably why my fighter hit % isn't where I think it should be, despite knowing my gunnery has improved.
I shoot at whatever needs to be shot, regardless of what "mode" I am flying in. I'll mark GVs by firing into trees, help deack towns or shoot buildings down if I am in the area and others are asking for help, especially if there are no air cons around. Clearly that hurts your score, though.
Maybe I should start saying: "No, sorry guys, I'm in fighter mode and I'm really trying to boost my hit percentage. I can't help deack. I can't mark that Tiger for you. I can't strafe down the VH. I can't shoot the troops. Because my hit percentage will suffer."

I'll never do that. I'd rather be a team player.
Just another reason why flying for score makes no sense in my book.
Does shooting airplanes in Attack mode hurt your hit% as well?
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Ryno