Hi, I'm the author of this app. The notes on each client are stored in an SQLite database for performance reason. If they were stored directly as text files it would be slow to query them, it would be very hard to make it work on mobile (and even slower), and you wouldn't be able to easily create relations between notes and tags, notes and notebooks, resource links, etc.
It's when exporting them or syncing them that all the app entities (notes, but also notebook metadata, tags, etc.) are converted to plain text files. One advantage of this is that the notes are not locked into an obscure format - it shouldn't take more than 1h to create a script that read and convert these text files to any other format.