I am not sure that I know precisely what you mean by "waterproof-glued plywood" but from the context I assume that you are talking about marine plywood and not epoxy saturated cold molded plywood. Marine plywood makes a lousy core material. Once water gets to the core, rot is able to spread in two directions at once and so the core rots and delaminates very quickly. There were some schemes where small blocks of plywood were encapsulated into decks as a core material but again rot is able to spread in several directions at once so I would shy away from boats built using that technique. Additionally Plywood cored decks tend to be heavy and so increase rolling and reduce stability. For better or worse, plywood is nearly universally used in high stress areas of cored decks such as mast steps and winch bolting areas.
End grain balsa makes an excellent core material. It is light and offers a high fatigue and sheer strength. The whole concept behind end grain balsa is that the open pores at the ends of the balsa cells allow resin to soak into the wood and seal the pores as well as establish a strong adhesion. In theory the risk of rot is greatly reduced in end grain balsa because the cell ends are sealed and since rot in balsa (like most woods) can only spread in the direction of the cells. Of course we all know that balsa cores can and do rot when they have not been properly sealed.
So to summarize, I think that plywood is very inferior core material usually employed as a money saving measure. Balsa core is a very good core material but should be sealed from moisture when a new hole is drilled through it, and moderate to high density foam cores are the best material in terms of durability.