I haven't played A Link Between Worlds yet myself, but it is safe to say that inconsistencies like this are bound to show up. I'm not sure why the Hylian Sheild cannot be where it is in that game, but I assume there is a logical reason from a developers standpoint. Like, maybe at that point in the game they deemed it time to upgrade your shield. Or maybe it is possible for you to loose that shield (via Like-Like for example), therefore you need somewhere to go to repurchase it? I suppose the developers could have taken the time to create a new shield, but who knows? Like I said, I haven't played A Link Between Worlds yet so I am not all that familiar with the issue.