For score purposes, proxies count as much as any "regular kills", i.e. they will increase k/d, k/h, k/s. The main difference in that regard is, that they give you only 1 score point (usually you will get hundreds of points for a "real" kill.)
However they do have the same category restrictions as other kills, so if those proxies were GV's towering out while you were flying in fighter mode, they are not counted for score.