I don't see why you say he stonewalled the investigation. Other than texts that show McNally was, at one point or another deflating footballs, there's also zero evidence that any of this ever happened.
That being said, those texts alone prove there was a concerted effort between Jastremski and McNally (at some point).... After the Jets game, in which some of the balls had been inflated by the refs up to 16 psi, Brady made a comment about McNally: "Isn't it his job to make sure this doesn't happen?" (Paraphrasing). You could take that any number of ways. Brady figures it's McNally's job to remind the refs how he likes the balls? Brady has intimate knowledge of J and M's shenanigans, and is being a little cryptic about it (which is generally how people talk when they know they're talking about something seedy)? Or, Brady is completely ignorant, and doesn't even realize McNally is just a ball boy? For Jastremski, you have to think giving your boss "plausible deniability" with something like this is important... perhaps Brady was allowed to be willfully blind... "You like 'em soft, we'll make sure they're soft champ..."
I was always interested in that text between Brady and Jastremski where Brady tells him "you did nothing wrong." (It's important to remember there's zero proof any deflating happened for the AFCCG, and so for that game Jastremski and McNally perhaps didn't do anything wrong.). He says it to reassure him: does he just mean "hey, you're not in trouble because this time you did nothing wrong"? Or again, maybe Brady is just totally blind/ignorant/naive... it was a pretty robust rumour around the league that NE balls boys were doing this, you have to think Brady would at least have an inkling, then again he's a pampered superstar QB, and getting to be ignorant of whatever cheeky crap your underlings do to help your performance is part of the pampering.
In the end, you're absolutely right, deflated footballs are meaningless, a fact that seems to be getting lost in all this.