If there is enough demand, a remake could be produced.
Zelda Producer Eiji Aonuma has mentioned that if there is enough of an emotional response, a 3D remake of Majora's Mask is a possibility, he stated in an interview on Nintendo Power.
The exchange went as follows:
Nintendo Power: After playing Ocarina of Time 3D, the next question that comes to mind is: Will we get a Majora’s Mask remake next?
Eiji Aonuma: Would you like to play such a remake?
NP: Well, Yes!
EA: It’s been 13 years since Ocarina of Time was originally released, and one of the big things that we made this remake possible was that there was an outpour of emotions from people who said they would like to see this game done. We said we could do it in 3D, so we did. I think certainly if there was a similar output of emotion and clamor from fans for a remake of Majora’s Mask, it wouldn’t be an utter impossibility.
Thinking on it now, having a handheld Majora’s Mask where you could kind of just set things down on your own time – close it, set it aside and come back to it later – might be a game play element some fans will actually take to and might really appreciate. Especially considering how you really had to rush through the original game, in a sense.
The Legend of Zelda: Ocarina of Time 3D has been well received by critics and fans alike. It sounds like with enough demand, there are no technical obstacles that would prevent a 3D remake of Majora's Mask going ahead.