SQLite databases created by PSPDFKit are not encrypted by default. They are still protected by iOS Data Protection just like all application's data. In case you need to add additional level of security there're SQLite extensions that enable database encryption. These extensions encrypt database content and SQLite metadata.
One of such extensions is SQLite Encryption Extension. This extension requires SEE license.
You can read more about how PSPDFKit integrates with your custom SQLite library here.