An application being powered by a single SQLite database file is better than being database-free.
The one .sqlite3 file is much easier to backup than a folder full of files.
For example, I prefer MediaWiki backed by a SQLite database over DokuWiki which stores articles directly in the file system.
@njoseph OTOH, if it's a bunch of files, you can keep it in version control easier.
@njoseph Use cases, though. If you want to do file sync with, say, syncthing or Nextcloud, a flat file/folder structure is highly preferable for a personal wiki. A sqlite file would practically rule it out because version conflicts would usually lead to data loss, much less likely in the filewise case.
The social network of the future: No ads, no corporate surveillance, ethical design, and decentralization! Own your data with Mastodon!