Some of them will tell you up front they will refund if the ship doesn't make it, however these excursions are EXTREMELY popular and fill up quickly. As for booking that day? I think you're really taking a chance.
If you want it I'd call as soon as the Disney lines permit (I think its 60 days in advance) or call Blue lagoon. I think you can do them WAAAAY in advance. The swim sounds like it would be much more fun than the "encounter".
Cheers,
Grumbo