If you have thousands of notes in a folder
~/my_notes
~/my_notes/work
~/my_notes/music
etc.
Joplin takes them and stores the notes internally as a SQLite table with UUID named markdown files. It makes it very difficult to use bash tools, finding them, other IDEs, etc to work with your files after Joplin has ingested them.Compare this to apps like VS Code / Obsidian / Logseq (also open source) which don't mess with your markdown file organization. You can just point them to a root folder and they'll work natively with your markdown files.
Furthermore, embedded media are also renamed to GUID.ext files and then are stored in ~/.config/joplin-desktop/resources which is terrible since now are notes are split from their related media.