I'd fill and then re-gelcoat (presuming your top is the original gelcoated fiberglass and not painted) (OTOH, if you plan to paint the top, then I would just fill and paint). If the holes are "deepish," or have core that needs sealed (probably not on vertical side portion) you could fill with thickened epoxy first; if not you can just go to gelcoat. You may want to make the first fill with a thickened version (you can cut up some small fiberglass fibers, for example) and then "plain" gelcoat over that. To match the gelcoat, start with the basic white base product and smear a bit (uncatalyzed) onto an adjoining area, then if it doesn't match add tiny bits of pigment (on a piece of plastic or etc., not to the smear on the top) and "re-smear" (the smears will wipe off with a bit of denatured alcohol) until you have a match, then catalyze, apply, let harden, and sand smooth. Before starting you should wipe with a solvent wash and clean towels in order to remove mold-release wax. Marine stores and online shops will have "starter" gelcoat kits that contain a small amount of white gelcoat and little containers of the basic pigment colors.
If you decide to plug the holes with screws, I would encourage you not to use silicone but to instead use something (anything!) else (polyurethane caulk, butyl caulk, butyl tape, etc.). Silicone is not only not very good at doing that type of job, but worse, will contaminate your gelcoat (or paint) and make it nearly impossible to re-caulk, re-gelcoat, or paint -- even years down the line. Getting it off (and the invisible oil it leaves) is.....
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