for most card there will be no hit at all. on the high end new cards your looking at 1-2% at most.
pci-e 3 just adds optimizations and opens a little more bandwidth but the reality is that most cards wont max out a pci-e 2 socket never mind a pci-e 3... so its only gonna become a factor when pci-e 3 becomes close to saturation. then you would see a 30% hit on a pci-e 2 slot (assuming the card still worked)
Oh really wow so the slots have been staying well ahead of the what the cards can put out. Makes sense.