True that the decision only really addresses the procedure followed and not directly the guilt or innocence. But if you take the time to read everything the Judge has said he does indirectly question that Brady had any knowledge if something did happen. Further, the way the investigation took place makes any conclusion as to Brady being involved ridiculous. It was seriously flawed in more ways than I am going to try and list.
There is never going to be any connection to Brady in my opinion because he did not direct anyone to do anything against NFL rules, meaning he never knew or asked for balls to be deflated after the Ref's inspected them. (And that's IF the balls were deflated) There has been literally no evidence even with the NFL trying to slant things that shows that.
The murkey part is not did Brady know, it's did something against rules happen. Because there is no record of what the inflations were before the game started, the Ref's kept none, and because two gauges were used that gave different results, there just can never be any even good circumstantial evidence something happened. Worse it was never documented which gauge was being used when. All that by the way shows how little the NFL thought the actual pressure mattered.
Combine that with proof the footballs were all or maybe all but one within the limits of what you would expect them to be with the natural loss of air based on weather and this has been a misdirected investigation by the NFL from the beginning.