It is still going to be getting wet inside. Waterproof glues like Titebond III are still able to absorb water over time. You need a glue that cures chemically and not by evaporation. Titebond III will work but is not ideal for watercraft. They even warn that it is not for use below the waterline.

As for coating plywood, yes the glue is waterproof, but you have to coat the wood with some sort of waterproofing agent in order to keep the wood itself from absorbing water. If not, then the wood layers will swell and shrink as they wet and dry and will cause delamination. You could just coat it with polyurethane or marine varnish.

I never trust a waterproof glue that cleans up with water. Bolder Bond makes a low foaming polyurethane glue that is waterproof. It would be a good option instead of epoxy.