So what’s the problem? First, those search results showing up on PACER aren’t just indictments, they’re court proceedings. That certainly includes indictments, but it also includes search warrants, records of petty offenses (like speeding tickets), wiretap and pen register applications, etc. For example, here’s the search page for criminal case reports from the Colorado district court, where you can see that “case types” includes “petty offenses,” “search warrant,” and “wire tap.” (There are other options as well if you scroll — although I didn’t take a second screenshot — like “pen registers,” “magistrate judge,” and finally “criminal.”) In the Q crew's instructions for conducting these searches (linked above), they specifically mention leaving all default settings except for the date, which means their search results will include speeding tickets and search warrants and everything else.
Second, the number 45,468 comes from adding up all the sealed court proceedings that are submitted every month. It doesn’t account for proceedings that have since been unsealed and/or carried out. In other words, that number is literally meaningless. It’s always going to get higher and higher, because they’re not keeping track of the number of court proceedings that are currently sealed, they’re just adding up the new proceedings that are filed every month. So how many are still sealed? Frankly, I have no idea, because I have zero desire to go through all 50+ district court websites (most states have more than one) and count them all up.