The great thing about applications that use sqlite as their application file format is that you can write secondary apps and utilities to supplement the applications themselves.
For example, Adobe's Lightroom uses sqlite as their application file format, which means that it's almost trivial to write an application to help it do things it's either really bad/exceedingly slow at (like removing images from a catalogue that no longer exist on disk) or literally can't do (like generating a playlist of files-on-disk for a specific collection or tag), without being locked into whatever janky scripting solution exists in-app. If there even is one to begin with.
All you need is a programming language with a sqlite connector, and you're in the driving seat. And sure, you'll need to figure out the table schemas you need to care about, but sqlite comes with sqldiff so it's really easy to figure out which operations hit which tables with only a few minutes of work.
Good luck reverse engineering proprietary file formats in the same way!
It's very annoying when the applications use sqlite with encryption. That is not open source, so regular language bindings can not be used.
I'm not sure how slqite as your application file format has anything to do with open source, honestly. It's certainly super easy for open source projects to use, but a closed source proprietary application using an encrypted sqlite file sounds perfectly sensible to me?
We all win when folks decide to leave it accessible, but I'm not going to hold "encrypting a file format so that people can't easily reverse engineer it" against folks who are trying to sell software.
I guess he/she meant that the extension that encrypts the database is proprietary. I believe that was the only option for a while but now there is an open source alternative.
Is the open-source alternative bidirectionally interoperable with the closed-source version (i.e. it can decrypt the proprietary encryption and the proprietary version can decrypt the FOSS version)? If so, then that's handy.
https://www.sqlite.org/see/doc/release/www/index.wiki
There are third party encryption approaches for SQLite. One of the most popular is SQLCipher:
https://github.com/sqlcipher/sqlcipher/
Those two don't have compatible file formats. eg no interoperability
Not sure if any others do, but yeah it would be handy if there are.