I was having exact same observation, albeit from a bit diffrent perspective: SaaS. This is where as the code tends to be temporary and very domain specific, the data (files) must strive to be boring standards.
The problem today is that we build specific, short-lived apps that lock data into formats only they can read. If you don't use universal formats, your system is fragile. We can still open JPEGs from 1995 because the files don't depend on the software used to make them. Using obscure or proprietary formats is just technical debt that will eventually kill your project. File or forget.
My 10+ year old photo management system [1] relies on the file system and EXIF as the source of truth for my entire photo library.
It’s proven several times over that it’s the correct approach. Abstractions (formerly Google photos, currently Immich) should just be built on top - but these proprietary databases are only for convenience.
For work, I’m having the same experience as the author and everything is just markdown and csv files for Claude Code (for research and document writing).
[1] https://github.com/jmathai/elodie