On my boat getting ready for the Texas 200, I added two 6" inspection ports in my cuddy cabin floor to provide water bottle sotrage lower in the hull. I also secured a bag under the floor to keep the water bottles from moving around. I used inspection ports so I could seal the inner hull back up and keep water out of there. On the Texas 200 we had to start out with 14 gallons of drinking water for our six days of sailing. There was a lot of other stuff to pack in the cuddy cabin as well.
It seems to me, rather than cutting the floor away, that someone wanting to put something large like a battery under the cuddy floor could install a rectangular storage compartment that would seal the flotation compartment to keep water out. I've seen rectagular storage unit inserts in West Marine's catalog, and I'm sure there are other sources. I think it is a good idea to get heavy items like a battery low in the boat.
John