This is only sort of true. You can import/export markdown(or text) files, but the source of truth is in a sqlite database. When you sync with webdav or another folder, that's also markdown - but it's not recommended to edit those files directly.
Other than that, Joplin is great. It's my main note taking app outside of spacemacs/org-mode.
It's FOSS, works on local files, has encryption and supports note linking.
It also has apps for several platforms.