I personally feel the only truly non obscure format are plain text files and it should be possible to use hierarchies, tags etc. with a combination of folders and front matter on the files itself. But I am a bit extreme in this, since I just don't like to migrate my notes yet again and have to install app after app on every device I need to access them. I was quite taken with projects like grav, that can provide functionality with just markdown files. But I haven't investigated to far on performance, especially not on mobile.

And you are right of course, that SQLite is quite preferable to most propitiatory cloud storage solutions.