Zach's posted on his blog
to confirm that he will definitely be in the next movie.
It's perfectly understandable that he wants to concentrate on other things for a while. The last few years of his life have revolved around Trek and Heroes and for the sake of his future career he needs to get out there and diversify a little bit, prove he's not just a scifi guy. Look around at most of his Trek co-stars and their careers are on fire at the moment, he's been unable, until now, to take advantage of the hype from Trek because of his commitment to Heroes but now that they've wrapped the season he can finally spread his wings and take on a new project. I know he's talked about wanting to get back into theatre work and that his next role would probably be on the stage so I guess we'll have to wait and see.