That's exactly what I just built for myself. Flatnote, on the windows store (and soon on mac/Linux/mobile) is a rich-edit note app which stores files as .md files in the file system. Sync is handled by just putting your notes folder in Dropbox
That's also why having a local SQLite is useful because you can more easily compare your local state to what they have.
I do have a local database store, but the Windows Store app is written in JS so I'm using NeDB which is basically just a mongo style interface for a JSON file. At the moment I really only use it to track recently opened files.
On other platforms I'll probably use SQLite, but I won't be storing the data in there, just the metadata (access times, paths, previews, wordcounts etc)
As one dev to another I have to say I love what you've built in Joplin. I love the name, I love the terminal app idea (Why didn't I think of that!) - its really a great achievement. You've built for multiple platforms and here I am hijacking the thread to peddle my half-built markdown-editor-with-a-file-list =D
(1) https://play.google.com/store/apps/details?id=com.ttxapps.dr...
Not open-sourced yet but will be very soon