No, there is nothing the water can do to damage the boat. It is after all a boat and designed to get wet. "But," you may ask, "what happens if you hit something?" I use my boats hard. I land on rocks, slide up on beaches and hit things. While it may appear that that the wood is right there where it will be easily damaged, it is an illusion. Actually the wood is under a layer of fiberglass cloth set in epoxy.
This may be hard to understand when what you see is wood, but you are actually looking through a layer of glass fabric. This is not just a little bit of epoxy or polyester resin, but actual glass. Like what you have in your windows. It is in a fiber form that is woven into cloth. This cloth starts out with a white appearance, but when the epoxy resin is spread over this cloth it becomes completely clear. This provides a huge amount of protection for the wood.
It is possible to scratch the outer surface. Just like any boat, if you hit something you can expect to get a scratch. But, it is actually quite hard to have this scratch be so deep that it actually hits the wood. It is very hard to hit something so hard that you actually get structural damage. Surface scratches are easily fixed with a new coat of varnish. It is not that the scratch needs fixing, other than for cosmetic reasons, but eventually you will want to apply another coat of varnish and most of your scratches will disappear at this time.