Put some structure back. A clone of the rib would be ideal.
However, the seat also provides torsional strength. Take the benches out, and the whole boat will corkscrew like crazy. If you are putting a deck in, this shouldn't be a problem, as you are replacing the structure (these will be tensional forces running diagonally across the horizontal surface - deck, bench top, deck structure, if stiff enough, and so on) but if you are leaving the entire boat open, you're going to get some flex.