Since you're painting the kayak, use silica mixed with epoxy and squeegee it on.

For a clear coat, builders are pretty much forced to fill with clear epoxy. Although gravity causes it to fill the depressions, it also coats the tops of the weave as well. Technically what happens is you finally flood the cavities until it flows over the weave. But a more economical way would be to squeegee it on and by using a filler, you will be filling the depressions faster. Just remember a sloppy job will harden like stone so care must be taken or you'll wish you never did that if you are grinding away lumps and high spots. Go over it with you fingers and level any high spots with a scraper during the leather hard stage.

The epoxy contributes to it's strength not just its abrasion resistance. Try breaking a piece of Okume and than the same piece coated with epoxy on both sides. Unbelievable difference. So the epoxy does more than make it smooth. It is adding stiffness, abrasion resistance and lateral strength as well.

If you haven't glassed, be cautious about blush. Use a blush free epoxy or make sure you fill soon as you can or as soon as the epoxy is non-tacky to the touch.