I guess it depends the person, dealing with sqlite + python doesn't need dependencies or custom drivers and is easy to do/easier to manage for me than bash scripts
But rather than having a self explanatory markdown & flat file, now I have to start learning about the schema & making specific tools (in my preferred language) for manipulating Joplin's schema.
Suddenly I'm digging through 20 different technic specs to decode what data is where, how it works, and what I can do to it. Want to edit history? This is the best help you'll get, pray it's adequately technical to expedite you to your purpose: https://github.com/laurent22/joplin/blob/dev/readme/dev/spec...
As I began with, I struggle to imagine anything that generates anywhere near as much user agency as flat files and markdown. Having boring common data & systems lets me apply portable skills I already have, rather than having to skill up in some particular product's own ecosystem.