Notesnook: A Private Note Taking Alternative to Evernote
blog.notesnook.com
blog.notesnook.com
If Notesnook ever gets as many features as Joplin i'd consider it as Joplin's UI is slightly wonky, but looking at the page it seems behind in terms of features.
There's a lot missing in Joplin. Notesnook is not going after Joplin though; it has already crossed it in terms of privacy, security, portability, and UI.
The most reliable way would be to send notes from external sources into an "inbox" of sorts; this inbox wouldn't be encrypted. Later on, when the user will open the app it would move and encrypt everything in the inbox. This is not secure or private at all.
Your idea seems good as well; a command-line helper app responsible for encryption.