You’re right that there’s no absolute facts here, but I imagine he did see everything he was taking because it seems he didn’t have a problem with what the NSA does (he went to work for them, after all), unless it is unconstitutional or undermines the operation of the internet as we know it. He chose the things he took for their specific meaning in the broader narrative. I’m sure he saw a hell of a lot of insane, scary things that he did deem to be within the reasonable operations of the NSA’s mission which didn’t make it to the trove he took.
I imagine he used those tools to scrape the NSA intranet, then went through when he got to see what was important to make his case. In the end: who knows… I just hope his life in Russia is reasonably tolerable.