Yes. Only the data is stored in databases (MongoDB or SQLite). All the definition files are stored in
/storage/collections/*.collection.php/storage/singleton/*.singleton.php/storage/forms/*.form.php
Data are things like
- users, some addon config, dashboard settings… -
/storage/data/cockpit.sqlite - collection entries -
/storage/data/collections.sqlite - singleton data -
/storage/data/cockpitdb.sqlite - form submissions -
/storage/data/forms.sqlite - locked entries (multi user setup) -
/storage/data/cockpit.memory.sqlite
Good question 
I don’t think so, but now you know it.