Hah, you think HN would use something mainstream like mysql?! I don't blame you.
But HN is 100% custom software, and built with it's own programming language as well, Arc (on Racket). AFAIK, HN still runs on files-as-a-db. You could check out the source here: http://arclanguage.org/install
That release is quite outdated. They added a lot of stuff to filter spam, voting ring detectors, and other moderation stuff. Anyway, as far as I know, everything is still saved to the file system.
Nope, I'm not implying it's bad, just that they used to do that and they still do that to this day. I have nothing against storing data in files. In fact, I do that all the time myself too.
Yes, ultimately they do (usually) and yes, you are missing the point.
"filesystem as a database" is not referring to database software that stores the data on disk but rather that the application is directly interacting with the filesystem. Imagine dumping a JSON document to disk, then reading it from disk, compared to storing a JSON string in a DB. Sure, they are both backed by the disk, but one is not "filesystem as a DB".