Theyse may have been caused by air-bubbles
Although a boat builder (try Mr Collignon of Fiberglass Hawaii in Santa Cruz CA) may have insights, it obviously when the gelcoat was sprayed nto the mold, some voids were there. Warranty work is best if the boat is new, If not I would fill with color matched gelcoat. ALthough you will have wax in these pinholes, you should be able to flush them our with a little solvent (use xylol or "grease and wax remover") the fill with gelcoat, if you can slightly roughen the inside even better, but it's only a cosmetic fix and not structural. The alternative of drilling them out etc is not worth the effort. If you go to the gelcoat and plastics forum, you will see a little essay I did (Fiberglass Trilogy II) on color matching gelcoat etc. I suppose you could also use a little tube of epoxy since these are so small but gelcat would be best because if can dissolve and "float to the top" any remaining traces of wax. Thanks Jim W
