The tracking dots certainly made things much faster for the NSA: they could immediately locate the printer and the date, without the need to audit the huge number of printers and employees they have. You say "on any given day" but they wouldn't know the day, only a rather large possible range of days.
I doubt that more than a dozen people printed that document. It was a TS/SCI doc IIRC, so all of those printers are in SCIFs with rigorous access control, so it's not like someone grabbed it off the printer -- you have to release the job from the printer console anyway.
How exactly would auditing all prints even work, assuming they were even logged? Wouldn't the auditor need to have security clearances to see what pretty much everyone in the NSA is working on, which goes against need-to-know principles? Or I guess an auditor needs to know these things to do their job...
