As Walt Jr mentioned above, one of the old wrecked ships is still in the attraction.
In the most recent installment of the Official Disneyland Resort Video Podcast, Tony Baxer says that the first wrecked ship you encounter in the ship graveyard is the same one from the original attraction, and that although the sea serpent isn't around, you might be able to see "evidence" of him:
"Going into the Graveyard of Ships, if you look closely, the first wrecked ship is actually one that was part of the original ride. And if you remember the old ride, the last thing that was in it was a good old sea serpent. Well, he's not there anymore, but for those of you who really believe in magic and if you look really, really hard, you might be able to find evidence of that sea serpent."