I have to agree with the theory that "Giant's Basin" (or whatever it's called) is probably the region of both lakes and the land between the two lakes.
Here's a Wikipedia article on "Basin":
Basins, as you will see, cover a lot of land. However, they are usually not entirely filled with water. They are emptied.
Thus, it strikes me as odd that a great body of saltwater would be called a "basin."
Maybe there was a few mistakes done on the part of the game designers.
Here's the Encarta Dictionary definition for "Basin":
A broad area of land drained by a single river and its tributaries, or draining into a lake
However, by "Giant's Basin", it might be referring to the lake(s) in a figurative sense. I noticed through my travels in the Guild Wars world that names often highlighted characters and lands figuratively, bringing a touch of humor to what would otherwise have been a ho-hum name.
A prime example is "Ettin's Back."
Is Ettin's Back a "back"? Of course not. It's barren land. One could say it's a canyon, technically. But that doesn't matter. The point is that the area we know as "Ettin's Back" is a barren land named to add a little humor to the area.
Just some things to think about...