Honestly, I don't think it really matters what happens, the ship will still be here because there will always be new people coming into the fandom. And not just because it is slash, or because it is Snarry, (although I like to think this ship will go on because it is one of my favorites) but because it is Harry Potter.
I'm not saying it is the next Star Trek, Star Wars, or anything like that but these stories got children to read again, inspired them to put down the video games, to pick up real books once more and to follow something that didn't require batteries. That's not something that happens everyday, so anything that keeps the story alive, I think, will endure regardless of the form it takes.