In other words, you have tiny holes in the deck seams after you used a filet and tape on the underside of the deck? I don't know what you would fill them with other than epoxy and since you have stitch holes as well it would seem that your epoxy top coat will fill them fine. Almost all builders just coat their outer surfaces with epoxy or epoxy/glass and allow the epoxy to just automatically fill the stitch holes and in your case the others too. If you try to fill individual holes in any way, it usually creates a visual mess and a lot more work for nothing.