Brady knew about those balls. .
He knew that they were footballs, and he knew that they were never tampered with, because they were not.
In Berman's decision he of course cannot say anything about the facts of the case (THAT WOULD BE GROUNDS FOR APPEAL IF HE DID), just how that procedurally the NFL messed up (no notice, making a witness and the actual data unavailable to Brady, the absurdity of a punishment for general awareness, etc.)
But five times he mentions the Wells investigation and uses "independent" and puts it in quotation marks every time! Whenever he mentions the 1st half footballs, he calls them "the allegedly deflated footballs". He quotes Wells on the admission of having no conclusive evidence. It's pretty clear that, if he could, he would have slammed the entire investigation because he thinks that it was rigged from the beginning. He doesn't open that can of worms, because he can't, but he sure left a trail of not-so-subtle hints!
After 7 months, someone in authority took a serious look at what the NFL tried to pull off!