You forgot about Four Swords Anniversary Edition for 3DS 
The thing is that there's two different inhouse studios involved in the remakes. The ones for 3DS were made by Tokyo EAD 1 and Grezzo, while Wind Waker HD was made by EAD 3 in Kyoto.
EAD3 is currently working full force on the new Legend of Zelda and has Tri Force Heroes as a side project, so it is rather unlikely that we'll see an HD remake from them any time soon. They may do one just to get the hang of the NX, but I'm thinking that's just going to be the port of the new Legend of Zelda for WiiU. So my guess: they're not working on it.
Tokyo EAD 1: we don't know what they're working on at the moment. It's a smaller inhouse studio which makes the 3(DS) guides, like the one for the Louvre. They have worked with third party Grezzo on three occasions: three Zelda remakes for 3DS. They have probably started working together with Grezzo on a new project. My guess is that it's Zelda related and probably Twilight Princess HD or Four Swords Adventures HD, but since Grezzo has only been working with GBA and N64 properties on 3DS, it would be a big step for them to remake Twilight Princess for WiiU and/or NX. Maybe they will get to remake another N64 title before that? We'll see. Maybe we'll get Four Swords Adventures first (so they can get to know the architecture) and then Twilight Princess.
Btw. about 5 days ago I made a thread about what Nintendo's inhouse studios are (probably) working on. You should check it out
http://gamrconnect.vgchartz.com/thread.php?id=205414&page=1#
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