Legally speaking, there's nothing stopping Rare from releasing a Banjo game on the 3DS. But all that means is that it's technically not impossible; it's still highly improbable.
For starters, Rare used to have a team dedicated to handheld development. That team eventually shifted their focus to XBLA development. This team no longer exists. Rare merged all their teams during the development for Kinect Sports. It's possible that they have since broken up into teams again, but it's unlikely that they would've broken up into as many teams as they once were in. I'd say two teams, tops. They obviously wouldn't bother reviving the handheld team, who, with the exception of the DKC/DKR ports, haven't made a very successful game. Not in the MS era, at least. Without the handheld team no one else could make it.
Assume that handheld team does come back from the dead. Like their GBA/DS games, Rare would have to find an outside company to publish their game, as Microsoft wouldn't. Sabre Wulf, Grunty's Revenge, Banjo-Pilot, It's Mr. Pants, and Pocket Paradise were all published by THQ(I'm using "publish" quite liberally; THQ did fuck-all to advertise the games). THQ no longer exists, as most of you know. Without them to publish it, who will? To be fair, there's nothing stopping any third party from publishing it, but with the sales of the non-DK handheld games, would Microsoft even greenlight another handheld game?
I want a Banjo-ThreeDeeie as much as the next guy, but we have to be realistic.