I still think it will look pretty decent. Now, correct me if I'm wrong, but didn't most SNES games simply simulate the "underwater effect" with sprites? Super Mario World, Donkey Kong Country, Mega Man X, etc. just had the hero enter the water but it didn't distort any of the images yet you could still tell they were underwater. At least, with having the transparent water tiles as a high layer over the entire map you want submerged, you get a better illusion of being underwater than those previously mentioned games because 1) Zelda is viewed from a bird's eye view camera angle and 2) you actually see the water moving over the level. So I think it's a good thing for the moment and just as aesthetically pleasing.