All damage is equalized among players in PvP. So, perks like "Upgrade Damage" are meaningless. Does this also apply to perks like "Glass Half Full"?
I was able to test this today. I used the Vanquisher VIII that you buy from the New Monarchy vendor.
Normally it does 22 damage when you hit the opponent's body. The bottom half of the clip did 23 damage, so Glass Half Full does work in PvP.
I wasn't able to tell how much headshots increase in damage, but I would assume that it is by a similar amount.