Hey, When i installed my hoods pins i did not scratch the hood. Although, the kit like mine had a chrome ring that went around the hole(On the outside of the hood), so if i had scratched it some it would of covered the scratches. I highly suggest putting some sort of paint on any scratches or holes you drilled so it does not rust(If your hood is steel). Good luck!
I have to do this for my 2" fiberglass hood because the car didn't come with a latch assembly. I'm kinda afraid it will blow open with just a latch anyway.