If the movie indeed makes it to theaters as planned, then yes there will be some merchandise. As far as what will be made only time will tell. If celebrities do some of the songs as has been rumored then a soundtrack album seems very likely.
Whereas if the movie is just direct-to-DVD (like Kermit's Swamp Years) then the merchandise will be much more limited. The main merchandise made for Kermit's Swamp Years were some posters, fast-food toys and the DVD.
For me, the great news about the movie is that it increases the likelihood that the remaining 48 Fraggle Rock episodes will be released on DVD since no doubt HIT would want to take advantage of the new Fraggle movie and promote as many Fraggle DVD's as possible.