It seems the amount of people logged on also may play a part in the score. I've noticed I earn more bomber points if my side is out-numbered by the enemy. I've used the same aircraft and bombed the same target at different times and noticed a differences in the scores. The only difference I could see was that on one flight we were out numbered (I fly Rook) and the other we out-numbered the bad guys.
So if perk points earned is any reflection of damage points then take JU-88s or a flight of Bostons and go to an arena where you are out-numbered.