If that small deck is open, sticking a mirror and a flashlight up inside might tell you what you need to know.
If the mirror doesn't answer your questions, and, since you are going to mount the trolling motor anyway, why not just drill a small hole? Watch for the wood shavings to come out.
As far as "two pieces of wood on the top"...I assume that is 3/4 inch plywood. That amount, plus whatever plywood is already there, should be plenty.
Many people are cutting fitted holes and putting in an aluminum tray so the pedal is the same height as your other foot. I sit so I don't need to put a tray in.