I think I see the problem. 99% of the site wasn't dark. That reddark site was showing a hand curated list of subs that announced they were going dark, compared to the number of those subs that did go dark. The exact numbers are impossible to track down, but reddit claims they have "100k+" active communities. Less than 10% of reddit actually went dark, conservatively speaking.

Of course, all subs are not created equal, so just comparing sub numbers doesn't tell the whole story, but even anecdotally, my sub list was mostly intact during the blackout.