Boats have wood structure under the glass. You can test it by drilling small holes in the stringer about a 5/16" drill bit will work. Go in about 1/2" and see if the wood shavings are black and mushy, if so, the wood is rotted. If the shavings come out dry and clean, its good. Seal the holes with epoxy when done to prevent water from entering the holes. The transom id the same deal, drill in deep enough to check the shavings but don't go through the outer skin. Check low in the transom and work your way up. Seal those holes with epoxy also.
Edit, What type of boat and year?