The problem with cove and bead is that it was popularized with canoe building which does not have the shear curves, bends and convex shapes that kayaks incorporate. When you do flush strips, just over-bevel a tiny bit favoring the outside joint.

If you do a pre-wet with water on your kayak, you might be surprised that it will look a lot better than you might have imagined. the wood will darken and the spaces or gaps will be way less noticeable. You can still fill a few but going over the whole thing with water putty is asking for disaster. Elmers wood filler comes in about 5 color tones, sands easily and is water soluable. I would try that if you have some larger gaps or with wood slivers filling gaps individually.

If it's a kayak your building, just let the epoxy fill any gaps on the bottom and just take care of the bow and stern end sides and the deck. Those are the areas that are most seen.