> directory tree is not as easy to view and edit as JSON.
tree path/to
cat path/to/key
echo "1" > path/to/key
But my point is that you're not using the file system as a database. You're using it as an index, and haven't considered about multiple readers/writers to those individual JSON files that are doing the real work as databases. It's kind of like writing JSON into a SQL table. You can do it, but probably not to store important data within that JSON that always needs to be queried and ser/deserialized for any kind of read or write. If you need that, you probably want NoSQL.
That's what tree is for
> I think it is only good to use directory as data table to store JSON data files, but not for JSON data properties.
I see that as no better than one big JSON file or a normal NoSQL database.
If you're really fancy then the whole DB is just a VFS and those JSON files aren't real files, just a serialized form of the DB.