At least now, months later, we learned the actual reason for the underwater dark portal in Azshara. Thanks to John Staats' WoW Diary, we learned that they just had no idea where to put the actual Dark Portal from lore. They initially put it on Teldrassil, but weren't happy with the location. So, they put it in Azshara for a short while, thinking it would be a cool location for it. They ultimately decided to put it in the Blasted Lands because there was nothing interesting there.
I was shocked when I first read that, since the Dark Portal had an explicit location in lore: the Black Morass of the Swamp of Sorrows. They were just lucky and placed it just close enough that they could retcon the location in a believable way.
So yeah, the underwater Azshara location? It wasn't an unused instance portal. It was a temporary spot for the actual Dark Portal. People weren't that far off with that guess, though. Old instance portals used the Dark Portal as a placeholder, which caused the confusion.
That was a really surprising detail he included.
Here's something I uncovered during a Q&A on Reddit with some of the original developers.
Here's something I uncovered during a Q&A on Reddit with some of the original developers.
This is something I am really hoping to do in classic. In Fact I would put this on the same level as downing KT