I have seen pontoon boats "submarine" , where the wave over the front
pushed the bow down and then the momentum drove them well underwater

Been there, done that. The first day I had my boat I got caught in open water
bringing it home. What happens is it submarines but then the prop comes out of
the water and you pop back out. After a couple of those I figured out
quartering the sea was the trick, just like most boats. I ended up "tacking" my
way home since the course was dead into the sea. That was the nastiest day I
have had on the water in this boat. Seas at about 4-6 and sea fog so bad I
couldn't see land. (with a Wal-Mart compass I wasn't sure about)
I would not have done it if I knew it was that bad. The water where I started
was fairly well protected. The only bad stretch was across the mouth of the
Caloosahatchee near that Sanibel Bridge we are arguing about in the $27,500
speeding ticket thread. It was about 2 miles of hell and I was back "inside"
again.