I agree you should probably remove them before painting. It's not too hard. I used a fairly sharp putty knife to get way under and sort of cut at the old epoxy.
I had mine powder coated with a black wrinkle finish. Seems really durable. I don't have any experience with the paint.
My fins were scratched up pretty good. I stripped the anodizing, sanded out the scratches, media blasted them to texture the spaces between the fins, polished the ridges, and then had them re-anodized. It was a ton of work, but they look brand new.