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It does, but if you use the build in synchronization, your notes will by synchronized as (optionally encrypted) files. I think using syncthing would be possible if you make Joplin synchronize to a local directory, and use syncthing to sync that directory.

I used to use Logseq with Syncthing, but I ran into a bunch of sync conflicts that were annoying to deal with and sometimes it would just stop syncing for no reason. Luckily, they've just made Logseq Sync available to all backers on OpenCollective and it works quite well. I'm very happy with the setup now. I think they're making Sync available as a paid monthly service soon.

No, Joplin stores files as plain text with obfuscated filenames. An SQLite DB is only involved for indexing and search.