I have a few #6 screws holding the acrylic down on my little single player cp.
I scuffed the heads and pushed them into a thin cardboard box, primed them, baked them under a halogen work lamp then painted them with a gloss black and baked them again. They haven't scratched or chipped, but they aren't under a lot of direct abuse, since they're countersunk in acrylic. When screwing them in I was just careful and didn't let driver slip out, and screwed it in by hand of course. You could probably paint up 20-50 of them at a time and store them in the same position poking out of a box in case they ever start to show signs of wear.