i found the issue; joplin doesn't adhere to the freedesktop xdg standard.
i configure these to keep a clean home folder, but joplin ignores these. I confirmed this by placing the files in the folder my os expects and voila, it shows up.
once i knew this was the issue, i found following github and forum posts:
for now, i will leave this as is, but i don't know if i'll be able to update joplin from within the app, now it's not in the expected directory.
should i not be able to update it, i'll use appimagelauncher.
but tbh, i do think, programs should adhere to this as it wouldn't break anything. everybody has these defined by default; i just changed the location of these variables.