Pats are betting the house that 1) no one within the organization will fess that they did it under Belichick's and/or Brady's order and 2) there is not video evidence showing a Pats official playing with the ball. The old 'no body, no crime' defense. This is clear because the NFL advised that it has hired an outside firm to review video evidence. If someone comes forward or a photo comes out, the Pats are screwed as they will get nailed for 1) breaking a rule, even if its enforcement was been poor over the years, and 2) lying about it.
I still think the best thing the Pats could have done was during the press conference would have been for Brady to say - "Yeah, I like my balls underinflated and had the equipment manager prep them. I've been doing it for years and so have most of the other QB's in the NFL. I'm sorry. It won't happen again." The NFL does not want this to continue to be THE STORY leading up to the Super Bowl. Brady fessing up would have killed the story then and there. No suspensions, no draft picks and a nominal fine and everyone could move on to the game itself.