OK I answered my own question.
I called the natural resources police at 301 645 0062. I advise you call them yourself because I wouldn't believe it from some forum goon with 3 posts.
What the guy told me is that the normal vehicle laws apply in md waters. If the houseboat is my residence, then it's a residence.
Then I asked the goofball question: Can I shoot clays off the boat?
Yes, he said, and i'm paraphrasing, you can shoot clay pigeons off the boat if you're not endangering anyone.
So I can go out in the middle of the bay and shoot clay pigeons?
Yes, he said, as long as you use the approved shot for duck hunting. (lead-free, i assume he meant)