Using Occam's Razor, I'd bet on the last option.

It's a false flag operation so reddit admins can claim they were attacked and take legal action against the protesters.

Or they took it offline to "hide" all the blacked out subreddits. Some had images about the third party apps as their only post, which was on the front page. By going offline it makes it seem like more of a technical issue rather than a protest.

I’d guess that with so many top subs going dark, the mixing algorithm needs to dig deeper and it’s not tuned for that. These algorithms are hard to get right at Reddit’s scale.

As an example to populate the frontpage or /r/all it might would need to scan all posts from the private subs before even getting a sizeable amount of candidate posts from the public ones to rank. Then the public subs won’t be in cache nor will caching help as much on those long tail subreddits. Not being in cache means more hits to the DB and that’s going to affect nearly all requests to Reddit.

It could be that their infrastructure is set up to optimize showing data on the typically most popular subreddits.