I used to use Joplin, I liked that it integrated with my Nextcloud, and the markdown format. However, the way that it handles the markdown files was too black-boxey to me, with the way it split them up in a weird scheme.
Now I use Ghostwriter with straight markdown files inside my Nextcloud folder. So I still get the syncing functionality, but a more flexible setup that doesn't require a specific app to access all of my notes.
I definitely prefer it over Snaps or appimages. Straight-forward to update, and Flatseal provides a nice GUI to control permissions (if needed). Themes may not work properly, but whatever, not a big deal for me.
The distro's repo is always my go-to. If it's not available there, then flatpak, and I'll use appimage under duress. If that doesn't work, I'll figure out a different solution.