It is indeed them. As the Going Merry goes up the Knock Up stream, there's a shot of Blackbeard's raft/ship being ripped apart and them all falling back into the ocean. I dunno if he reassembled it or just rebuilt it from scratch or what. It's a funny raft. There's definitely windows inset into the logs, implying that they're hollow. Then again, it is big enough for that and they do have to sleep somewhere...