Whether they did or not is irrelevant to participation in the game because of how not close the game was and because of how unnoticeable the PSI difference is, but, yeah, I think they probably did. Nobody with the organization will say anything either way until it's too late for the NFL to incur punishments beyond "We think you did this, you're paying us $X and losing a draft pick", though.
I think a lot of consistently successful sports organizations cheat in some way, it's just a matter of whether they get caught and when they get caught. For example, the University of North Carolina has been facing allegations that they created special courses exclusively for student-athletes that were either easy or where they could get a "tutor" to do their homework for them across all its sports over the past decade.