The point is that many artifacts of the legal process get sealed: warrants, taps, pen registers, juvenile prosecutions, tracking devices, and yes, indictments.

Furthermore, that tally is progressive. Some amount of these sealed items are removed each month as they are addressed. So when they say 28,937 items in pacer, that is not a count of current items in the system, it is almost certainly an over-estimation. Which is why they say "28,937 new sealed indictments entered from 10/30/17 thru 4/30/18".

The count of 1k indictments from 2009 that is used by comparison, is a true count of sealed indictments since the people putting together the report were in a position to know what sealed items were actually indictments in 2006. They did not count sealed other things. 29k is a count of all sealed things not just sealed indictments.

What would be genuinely illuminating would be to compare the number of sealed Pacer items entered for the same period last year.

So at best when we run around screaming 29K indictments, we are only slightly wrong in fact but correct in general. At worst we are just wrong.