My gut tells me it'll depend on how this film does, leaning toward original canon for the books, seeing as Star Trek XI is geared toward general audiences, and general audiences are less likely than dedicated fans to pick up a novel or comic book based on a franchise.
If this film is a huge commercial hit, then very likely novel covers and comics going forward will depict the new look and likenesses. If it bombs, I'm pretty sure Pocket and comics publishers will go on as if the film never happened.
"Now I did a job -- and got nothin' but trouble since I did it, not to mention more than a few unkind words as regard to my character, so let me make this abundantly clear: I do the job... and then I get paid. Go run your little world."