My thoughts on Spygate have always been this.
If the evidence only showed that the Patriots were filming the sideline signals, and that's what was announced and made public, and that's what they were solely penalized for, then why would the evidence need to be destroyed? If all the NFL found was the Patriots were filming in-game signals, and that's what you concluded and punished them for, why the rush to eliminate that evidence?
Answer: Because that isn't all you found and you knew that if what all you did find got out, you'd have a crap storm on your hands the likes the NFL could have never imagined.
You don't fine a team 3/4 of a Million dollars and take away 1st and 2nd round draft picks for something that, allegedly, everyone had been doing at that time.