If you have the plan, build it. It doesn't take much to resize the wood. If the ply is thinner than the balsa specified, add a little more length to the piece glued to it to compensate. For example, if the plan calls for 5mm balsa, you can use 3mm ply and add 2 mm to any piece that is glued to it at 90 degrees. With this design, the only places this will matter looks to be the bottom, between the sponsons, the transom and bow blocks.

Balsa will absorb water and flex, so even a coat of paint will not keep it dry. As it gets compressed and springs back, the paint or varnish will crack, leaving places for the water to get in to the wood. It's just the nature of balsa[]