While it does sound like the judge is concerned about the "independent" (his quotes not mine) investigation and adequate proof, the questions of contract and law addressed had nothing to do with whether or not there was cheating - the biggie was whether Goodell was allowed to use the "conduct detrimental" clause to apply the explicitly written PED punishments as his guideline for the suspension, rather than the explicit "tampering with equipment" punishment; and if Brady had been made aware that he was facing a punishment outside of anything he reasonably expected based on the player's rulebook he was provided instead of the coach/cwner rulebook which is what Goodell was working from.
Spoiler, he's not. And given the pretty strong, clear wording in the ruling, if anything is changed on appeal it's likely going to be slapping Brady with the equipment-tampering punishment of IIRC $5500 per squishy ball.
Disclaimer, Pats fan, ambivalent on the deflation - wouldn't surprise me in the least, but the "science" in the Wells report IS sloppy as hell.