..a counter sink type of tool in your drill motor and fill with white Marine Tex if they're not too big. If they were 1/4" or more I'd tape underside, fill with poured in epoxy with fibers in it, 'flange' the hole tops with a light application of your counter sink, then white Marine Tex over it.

Too large a hole I don't like to rely upon epoxy alone, hence the small chopped fibers mixed into the poured epoxy.

This will leave white 'circles' on the deck but good until you want to do more serious work.