The entire Great Flood story reminds me a lot of the story of Noah's Ark, in a way. You know, in order to protect/rid the world from evil, the heavens rained down and drowned the lands. Let those whose lives were spared--here's the twist away from the story in the Bible--flee to the mountaintops that became islands. However, the ocean didn't drain during the events of
The Wind Waker. That isn't to say it never drained as you don't see anything of the Great Sea after
Phantom Hourglass.
Though, I do think the Great Sea's water levels should have been dramatically lowered after Daphnes made the wish for the waters to drench the rest of Hyrule that was preserved beneath the waves. Water has a definite volume, so the logic in that is kind of absent. Though, I do recall that in
A Link to the Past, that it was stated by the "essence of the Triforce", a spirit who acknowledges you as a hero after you defeat Ganon, said this *shuffles through ZD's text dump*:
The Triforce will grant the wishes in the heart and mind of the person who touches it. If a person with a good heart touches it, it will make his good wishes come true... If an evil-hearted person touches it, it grants his evil wishes. The stronger the wish, the more powerful the Triforce's expression of that wish. Ganon's wish was to conquer the world. That wish changed the Golden Land into the Dark World. After building up his power, Ganon planned to go on to the Light World to fulfill his wish. But now that Ganon has been destroyed, his Dark World will surely vanish. The Triforce is waiting for a new master. Its Golden Power is in your hands...Now, touch it and think of the wish in your heart.
Analyzing that, I'd say that once the one who wishes upon the Triforce is lost in some way, the wish is reverted. So, the water level of the Great Sea perhaps did lower during the final battle, but after Link and Zelda leave the now flooded Hyrule, Daphnes is left to drown--and when the life leaves him, does Hyrule become dry once again? It's such a complicated concept with everything that goes on in all of these games. The most-annoying part for me is that the land of Hyrule is covered in water from the Great Flood, but somehow, there is an air pocket that preserves Hyrule Castle and allows it to remain dry.
I suck at developing theories for these things... So, I really don't know. I don't think the flood would cover the entire world that is seen in the Zelda games, because is it ever-changing and we probably haven't seen most of it. I mean, we don't even know where New Hyrule is in relation with the Great Sea, so... that proves that we can't even say how much of their world we haven't seen. But, anyways... another story
The Wind Waker reminded me of... the Lost Kingdom of Atlantis. Maybe instead of the world being flooded, Hyrule just... sank? I really don't know what to say. Nintendo's goal is to confuse people. ;s
