I read another Wolfram blog post where he answered those criticisms. http://blog.stephenwolfram.com/2012/05/living-a-paradigm-shi...
I don't think Bell's theorem raises a problem in either LQG and CDT because they have the traditional quantum theory built into them. They are not deterministic theories like Wolfram's. Bell's theorem discounts the possibility of quantum (as it is observed) if there were no long range connections defying locality.
Also, physicists don't generally take Wolfram's claims about how cellular automata are related to quantum or classical gravity or anything else in fundamental physics very seriously. A New Kind of Science cites very few sources and makes it seem like everything in there is new, which isn't the case. There was loads of criticism about that when the book was released. Nonetheless, it's an interesting idea and if something useful came from the work it would be good.