I was never able to get encrypted syncing working with Joplin. I tried every year or something for a while but it never worked. I kept looking for an Evernote alternative for years. The closest that got there is Leanote, which is a Chinese company's open source product. (https://github.com/leanote)

I finally gave up the search. Switched to unencrypted plain text md files synced with syncthing. On Linux I use Kate. It has a directory tree view and recursive search in said directories. It works great. On Android I am using Markor to point to the same shared directory. I don't think I'll ever start looking for a note taking app again. I also found I don't really take notes much. So there's that. :)