It has pretty much been confirmed that Countdown, Countdown to Darkness, Ongoing and the Star Trek Video Game are canon in the Abrams-verses based on interviews with Roberto Orci.
Since when? Orci's said repeatedly over the past several years that he accepts the standard Trek policy that only onscreen material is canon. There was that one time that Anthony Pascale at TrekMovie interviewed him and basically browbeat him into agreeing that the tie-ins should be canon, and Orci said "Okay, they're canon" basically to shut him up, and then retracted it a comment the very next day.
And there are plenty of things in the Ongoing comic that have been blatantly contradicted by Into Darkness
-- crewmembers dying in the first two storylines, Sulu holding the conn in a couple of storylines, Scotty continuing to develop transwarp beaming when the film said the tech was confiscated by Starfleet, etc. Countdown
had some inconsistencies with the first film as well, like painting a backstory of a Nero-Spock friendship when the dialogue in the film ("He called himself Nero") suggested they'd never met before their clash at the supernova site.
I've been following some of Orci's comments on TrekMovie lately, and frankly I think people take them far too literally and seriously. I think to some extent he just plays along with others' suggestions in a "Sure, why not, whatever you say" kind of manner, rather than issuing formal declarations of official policy.