Maybe it's just me, but I don't think references are worth thinking too much over. We know Ninty likes to throw these kinds of things in without any regard for continuity. Also, I don't think it's necessary for a Zelda game to add anything to the already incoherent lore, like I said, I think...
Really? For me, that would be my case for keeping it in. The fact that it just slides in without causing problems is quite remarkable for a Zelda game.