Not concerned about MDF as long as the execution is perfect (it's a long list), it's totally sealed and it's elevated to allow for drainage and evaporation. An MDO plywood or Medex fiberboard are constructed with solvent-based adhesives and are superior. A high grade birch plywood like MLA mentioned is also a great choice. It requires too many fiberglass layers (work) to get the same rigidity as .75 wood construction and to make a fiberglass enclosure adequately inert. Some fiberglass production boxes are great but are sprayed with a chopper which greatly reduces the time investment.
IMO, the JL Audio W7 series woofers are the finest reference woofers available...period. Incredible R&D went into these woofers. Every design is a trade-off. NO exceptions. The W7 is about extra controlled excursion, deeper low bass extension and a wide linear bandwidth. The cost is the extra power it takes to achieve those benefits, particularly in an open field boat. A bit less excursion and a bit less bandwidth can result in a greater internal efficiency. So if I was looking for a top subwoofer I might also consider the JL Audio W6 series specifically because it is a less demanding woofer to drive in an open field.
I would design my maximum displacement enclosure first that fits the boat and let that dictate my best subwoofer selection.

Earmark Marine