I don't think this "master" will be Malladus, since ST takes place in New Hyrule, which is a whole other land than Hyrule. The fact that Malladus has been stated to be some "ancient evil from long ago" doesn't mean anything refering to SS, in my opinion. It is more likely that he was an "ancient evil" related to the land that became New Hyrule.
Almost all evils in games are named as being some "huge ancient evil". It is just to make it feel more legendary. Thus, SS is Hyrules' backstory and ST is a story that takes place in a whole other land after Hyrule has been flooded. I think it's impossible Malladus will be the "master" Ghirahim is trying to resurrect.
I also don't think the "master" will be Majora or anything else relating to Majora's Mask, like the Feirce Deity, because Termina is, like New Hyrule, a different land than Hyrule and Majora is stated to be "an ancient demon sealed away in the mask and used by an ancient tribe for hexing rituals". And in general; Majora's Mask is a unique game and doesn't relate to any other Zelda game in such way. What happens in Termina, stays in Termina
Moreover, the word "demon" is used in many context (especially in Japan) and there isn't any known relationship between the different "demons", who has been used in the Zelda series. Majora was refered to as a demon and so was Aganhim (not sure), Malladus and I believe the OOT Shadow Temples' Boss Bongo Bongo was shortly refered to a some "demon".
Skyward Sword has been confirmed to explain why Ganondorf shows up in OOT, so I think IF we want to say anything about who Ghirahims' Master is, the most logic conclusion is that the "master" is Ganondorfs past live, some evil that will be reborn within 100 years or some Gerudo/Koume and Kotake related entity.
But appart from all this. I don't like the idea that Ghirahim will turn out to be just some dude trying to resurrect his master. I had expected this rather unique and flamboyant antagonist to be more than just some pawn of a greater power and actually having his own egoistic motives and being power-hungry himself.
I also don't like the idea of having a TP-like scenario in which the main-antagonist will be revealed at the end of the game.