Which is nothing new for these movies. Abrams massively overhauled mind meld between Kirk and Spock Prime in Trek XI just two weeks before the film's release, resulting in the destruction of Romulus being much different than it was in the working script available to IDW when they were writing the Countdown comic.I guess maybe they won't make one for star trek beyond because the script was subjected to too many changes and last minute additions while filming and doing reshoots.
Okay, Beyond's reshoots are a bit more drastic (they even cast a new character created specifically for the reshoots). But, the decision not to do a novelization was likely made before these reshoots were done. The reshoots were done in the winter. Based on how soon prior to STID's release ADF was contracted to do the novelization (October 2012) the final decision not to do one for Beyond would have been made in December 2015.
Besides, how many movies these days even get novelizations? TFA is the only one in the past year I'm aware of, and that's likely related to Star Wars being such a merchandising blitzkrieg. Aside from books movies are based on getting new covers to tie-in with the movies, I don't recall anything else.