Zelda: Wind Waker HD can’t use any dungeons that were missing in the original version. That’s because they were used in future Zeldas – likely Twilight Princess and/or Skyward Sword.
Aonuma talked about Wind Waker’s cut dungeons and the decision to avoid adding new ones in the HD re-release in an interview with Eurogamer:
“Quite honestly, those dungeons we removed we used in other games, so we can’t use them in this version!”
“I’ve received many questions about additional content beyond what was in the GameCube version of the game, but our desire is to stay true of the story that was in the original. If we add dungeons then that will affect other parts of the GameCube version, which we really want to stay true to. If it felt like there were maybe too few dungeons then I feel that what was wrong with the GameCube version was the pacing. It was thrown off because it took longer to get to certain dungeons. There was a waiting period, and then when you arrived there the experience maybe didn’t feel as big, as you’d waited so long to get there. We’re tuning the game to alleviate all that. The pacing should feel appropriate to the overall experience this time… We need to tighten those [gaps] and make the overall experience and story feel tighter.”
Unfortunately, Aonuma couldn’t reveal which dungeons were cut in Wind Waker and used in other Zeldas.