I don't think they will. He's one of the keys to traversing between worlds, and he's also right now the only connection to Wonderland, which I'm sure will be expanded upon in the future. I am surprised they wrapped up his daughter storyline so easily, though. I expected more difficulty.
But he's not the key, his hat is. And his hat is ruined now.
And he's not the only connection to Wonderland either, since while it hasn't been explicitly stated, it's been very heavily implied that Cora is the Queen of Hearts. Though they do still need to explain how the Mad Hatter was affected by the curse that brought everyone to Storybrooke. Did he somehow make it back to the Enchanted Forest? Maybe that could tie into how Cora got back to the Enchanted Forest. Or did the curse somehow reach him in Wonderland?
Plus I feel like the show is heading in a direction where the worlds besides ours and the Enchanted Forest will start to become more important, so I can foresee them coming up with a new plot device that lets them travel between worlds more easily than the hat or magic beans.
It's like in Lost, how traveling 50 feet down the beach was an epic journey that took several episodes in S1, but by S6 they're like, "Hey, we gotta go to this landmark on the other side of the island," and in the next scene they're already there. Or in Fringe, getting to the alternate dimension was next to impossible at first, but by the time I stopped watching they had literally just created a doorway between dimensions. Or in Supernatural, a significant portion of the first two seasons was about finding the mystical gun with limited bullets that was the only way to kill demons, but now they just have magic demon killing knives and slaughter them by the dozen.
I'm pretty sure there's a TV Tropes page on this concept.