Shigeru Miyamoto may no longer be the go to man behind the Zelda series, but he is still consulted and asked for his opinion time to time. That, and he's Shigeru Miyamoto—he pretty much knows everything going on at Nintendo, from games to hardware to board meetings. Due to Iwata's illness, which kept him out of the recent shareholder meeting, Miyamoto had a larger than usual presence. Through that presence, he all but announced Nintendo is currently working on a new Zelda game for the 3DS. At least, formulating the ideas behind the game if nothing else.
"In this way, we are gradually changing the structure of “The Legend of Zelda” series, and we are preparing to newly evolve the series for Wii U. In addition to that, we have ideas for Nintendo 3DS which we have not announced yet, so I hope you will look forward to them."
To understand this in context, he is talking exclusively about the Zelda series at this point in the meeting. It isn't really too surprising that at least plans for the next Zelda game for 3DS are moving forward (and likely slated for a 2016 release if I had to guess).
Source: Nintendo Japan