I have a personal theory that I posted to ZD a while ago and i was quite proud of it and I remember other people liking it and i dont think it was completely shot down as being something impossible for Zelda lore, so here it is.
What if Lake Hylia is the crater left in Hyrule where Skyloft used to be after it was lifted into the air?
That could be why its called Lake Hylia, sure the lake changes shape depending on the game but the lake has never been too big, with maybe TP being the outlier.
I liked this theory, its the only one i've come up with. It isnt true for Zelda (probably) but its fun.