Actually, no. Guybrush's ship was not destroyed. When we last saw it in Chapter 1, it drifted off to sea after he moved to Elaine's ship. And at the end of Chapter 1, his ship was already taken by Elaine and LeChuck.
Oh, yeah! For some reason I was thinking that the ship destroyed at Ch1 prologue was Guybrush's. Probably because of the way TheWelshman asked his question. Still, the crew's probably dead anyway