Zelda series director Eiji Aonuma has explained that the two dungeons that were left out of the original Legend of Zelda: The Wind Waker were actually used in parts for other Zelda titles that came after Link’s sea sailing adventure. Aonuma says he knows that fans have been requesting those dungeons be implemented in The Legend of Zelda: Wind Waker HD, but says that aspects of them have actually already been used in other Zelda games.
“I’m aware that lots of users wanted those two missing dungeons to be implemented in Wind Waker HD. But to be honest, we’ve already used those two dungeons for other titles after Wind Waker already. So right now, technically, they don’t really exist anymore…”
“We didn’t exactly use them as-is and implement them into another game. We’d add some [of their] features to other dungeons. So they’re in different dungeons now.” Elements of them must have found a way into Twilight Princess and Phantom Hourglass, but who knows – their remnants may be somewhere in Skyward Sword, too.”