My bow lockers are notoriously damp, not sure how water is getting in.
I really don't think any chemical will help if you get a hole in the sealing layer, what ever it is. If yours is still solid, I would glass over it after it has dried thoroughly. That won't protect it from below, but nothing is likely to damage it from below. If its feeling squishy at all, I'd replace with something that won't rot, or glass over a good marine plywood.