If the bolt is turning when you turn the nut, an impact wrench will sometimes tighten the nut on the bolt.
If the boat is off the trailer, you can try using a gear puller to apply pressure to a socket positioned on the carpet above the bolt head, which may hold the bolt enough to tighten the nut. Start with a larger socket than the bolt head to minimize damage to the carpet. Try smaller sockets as needed.
If there are enough bolt threads extending thru the nut, grip the bolt with locking pliers (Vice-Grips), and turn the nut with a wrench.
I have used all three tips with success. If the bolt is turning, it is probably due to the wood rotting. The 1st 2 tips may also work to remove the nuts.