Sure. But another line of thinking is that if you do a good job with marine ply, it will likely last longer than the stuff that is in there now. Personally, I didn't hesitate to use wood when I did my floor and bulkheads.
Just helped a friend rehab (entire floor, all 4 stringers, bulkheads, etc) a 1979 Mastercraft and used all wood there, too - and I KNOW we did a better job than the factory did in 1979!