I'm a backend server programmer, and although I have never worked on reddit I can imagine the conversation a few years back:

Dev A: How do we implement private? Should each post have a private flag or do we join on the subreddit to get it?

Dev B: that join might be heavy for the front page since we might have several different subreddits, a flag in each post is faster.

Dev A: But that means that whenever a subreddit goes private we need to flag all of the posts there

Dev B: yeah, but that doesn't happen often, the front page gets accessed millions of times, most subreddits never change status, especially larger ones.

Dev A: I guess you're right, even a large subreddit will be done in minutes, what are the odds of several large subreddits going private at the same time?