I think the rumor/report/whatever was that Nintendo had two Zeldas in the works for the DS, one being a Four Swords game, and the other being a new 3D game, built on a port of the N64's OoT/MM game engine.
I'm guessing that Shiggy or whoever may have announced that they know they're going to be making a "Four Swords DS", but work still hasn't technically even begun on it yet (possibly due to Twilight Princess's crunch time).
I should think that if they're working on a new Zelda with the OoT/MM game engine, it would have to be Nintendo, not Capcom.
NST could be working on it, as they already have experience with OoT/MM on the GameCube, and putting together the Master Quest, and experience with N64/DS porting (Ridge Racer DS). But it's probably just the grunt work, as I can't see Nintendo giving them an entire Zelda to design. Plus it's probably going to need an all-new non-cookie-cutter focus on game design, to make a 3D Zelda game that's built with a focus on D-pad or stylus control, unlike Mario 64 DS which was built around analog.