It's a near certainty in the long run. Nintendo has remade or re-released with new packaging several other games in the series without visible demand for them. Over 55,000 people have signed the petition for the game, and Nintendo won't ignore them forever. OoT 3d has sold over 3 million copies, and they'd have to figure that MM 3d would sell at least a million. Nintendo barely did any work for OoT 3d it seems with Grezzo doing most of the work, and MM 3d would basically be free money for Nintendo whenever they decide to cash in. I think they are saving the game for a rainy day when they are desperate and have few good new ideas.
However, you worded it as "on the way," and in that respect I much less optimistic. Who knows when they think it's the right time to remake the game. Right now they may have lots of other projects in the works and MM is not a priority at all. However history has shown that Nintendo can't help themselves from remaking anything with some level of popularity.
In the long run I'm about 99% sure some form of Majora's Mask will reappear eventually. They remade ALttP, LA, OoT, and WW with no one asking them to do so. They've given direct sequels to several of the games in the series- LoZ, ALttP, OoT, WW- and have even given a sequel to a sequel in ST. Nintendo can't help themselves from revisiting old ideas. Majora's Mask is one of the most unique ideas they've had in the Zelda universe, and I can't imagine a future in which Nintendo leaves the story of Majora's Mask alone forever.