Only drawback I can think of with hydroturf is working around the engine bay dividing walls and screws in the floor. Your boat may be different but my carpet went under the walls and there were a lot of screws holding down hoses/wires, hinges, etc.

Whatever route you go I don't think you'll miss the carpet AT ALL. I had a ballast drain acting up yesterday and it was nice just pulling the drain fitting off and letting the bilge take over without having to deal with soaking wet carpet.