If you are comfortable with a cli you could use gnupg. Its man page is good.

If I have cloud storage mounted somewhere I need to be able to drag and drop directories in and out, see the files inside in an unencrypted form, and they should transparently be uploaded encrypted. This could very well be achieved by a bunch of scripts involving gnupg, but then that’s what’s I’m looking for, because gnupg by itself wouldn’t be productive to use unless as a one-off.

This seems promising: https://szymonkrajewski.pl/encrypted-cloud-drive-rclone/