I'm 95% sure Nintendo will make a 3D (like OoT, MM, TP) game in 3D for the 3DS (then again, I was positive that Skyward Sword would be released when Nintendo said they would released, silly me).
Have you noticed that Zelda has been on every Nintendo console since '86? Why should they stop now if it means more money? But I'm sure thats not the only reason they'll make Zelda 3DS. Nintendo's probably noticed that they've been on every Nintendo console with Zelda since Zelda I, and they probably won't want to just stop with OoT 3D, 'cause thats not really Zelda 3DS, it's more like Zelda 64 on 3DS, like Link's Awakening DX was a Game Boy game on Game Boy Color. But Nintendo didn't stop with LA DX, did they? So they planed the Oracle trilogy (at the time "trilogy") to come out 3 years later (DX- 1998, Oracles- 2001 ?) Although only 2 of the planned 3 Oracle games came out, Zelda GBC game(s) came out.
Now, I'm not saying we'll see more than one Zelda 3DS game, and I'm also not saying that it'll take as long (due to today's technology). If and when Zelda 3DS comes out, it'll probably be something like Wind Waker. Not the flooded Hyrule and sailing and such, but the same graphical style. Or, they may choose to use the graphical style of OoT 3DS. I think Nintendo will use the latter. Also, I don't think it'll be a long game, such as WW or TP, but a shorter (and full of extras) game, such as SS and MM. And, lastly, if...if Nintendo makes Zelda 3DS 2 (I'm tired of hearing Zelda 3DS, too. No pun intended), it'll most likely be over-head, bird's eye, 2D view, like PH and ST.
Well....I've gone and gave a really long answer to a some-what simple question. Short Answer:
"I'm 100% sure Nintendo won't pass up this oppronunity to make a 3D 3DS Zelda. And I don't really think that we'll see more than one 3DS Zelda."
Did you know...?
Did you know that there have been 5 versions of the DS?
DS (original)
DS lite
DSi
DSi XL
3DS
Just a fun fact....