I think I would drill them out a little bit (maybe 1/32" bigger) to get rid of the caulking or whatever else is there. I would then get some epoxy (maybe even the 5 min type at HD), mix it up and start filling (from the inside of the hull) the entire hole and when you see it start getting to the other end, put some painters tape across the hole on that end and keep filling the hole until you see the tape bulge. Then tape off the other end and let it cure. Then I would lightly grind it down on each end with 80 grit making a little divot (concave) in the filler and the gelcoat around the hole and apply some Marine Tex to blend into your gelcoat (if it's white).
