Can your exhaust hose be routed very high before connecting to the exit pipe? I am assuming you are using a waterlift muffler. The two together should prevent any following seas from entering your engine.
I used to worry about this but it never happened. I think mid engine boats with side exhausts have more problems than stern exhausts.
I'm curious, why take TAPPAN ZEE all the way to Port Townsend to haul out? That's a pretty long commute for you.
Storm Along is hauled out at Oak Harbor right now for a bottom job. She should splash Monday.