But the judge wasn't ruling on whether or not the NFL had enough evidence or whether he was innocent or guilty. It was all about whether the NFL had enforced a penalty greater than what the CBA allows. He ruled with Tom Brady that they had gone too far, so his suspension was vacated.
None of the cases between the NFL and their players have been about whether they had sufficient evidence in the cases. It's all been about whether the white knight has the legal authority under the CBA to punish his employees in the manner that he has done recently. So far the various judges that have reviewed these cases have decided that he has acted improperly, and have overturned the suspensions he enforced.
All of the cases up to Brady were purely about unfair punishment, which is a ground for an appeal and court intervention on a legally binding mediation, which is what Goddell is per the CBA.
What is different about the Brady case was he not only found the punishment was not fair, but the investigation had "significant legal deficiencies"
It is a 40 page document that the judge issues, it is allot more than just saying he over punished Brady. There is a whole section that the wells report was supposed to be "independent" but was found not to be independent. The report (on page 5 if you want to look) talks about "there is less direct evidence linking Brady to tampering than either McNally or Jestremski" Meaning while they most likely did deflate the balls, there is no direct evidence Brady had any knowledge.
He also mention that the evidence they had, of the two Personnel being in a bathroom for less than 2 minutes with the balls and the lower pressure than the Colts balls "did not provide a basis for them to determine with absolute certainty whether there was tampering or not." Meaning there really isnt any direct evidence against the Personnel much less brady.
It also talks that Goddell should have agreed with being recused from oversight of the hearing, and as you point out, the appropriateness of the decision.
But make no mistake, it does find there is no direct evidence linking Brady, and the "general knowledge more probable than not" finding of the Wells Report. to be a complete over step of the boundaries.
So yes, in the 40 pages (if you read, because i have) of the judges ruling, it absolutely states there is no direct evidence against Brady, that is why it set aside the punishment completely.
PS, below is a link if you want to read the findings yourself.
https://www.documentcloud.org/documents/2329817-national-football-league-management-council-v.html