As outlined in How to store Joplin notes in Cryptomator it is possible to store Joplin notes in Cryptomator. However, I have not found a method to open notes stored in Cryptomator on iOS. The selection menu for sync does not offer local folders (which may contain the local Cryptomator store) but only a few cloud services. But these are not usable, when the notes are inside a Cryptomator.
Thanks, Dino. I saw that possibility, but I'd like to avoid a situation where I have an encryption scheme per application. The key management and repeated verification of verification algorithms would be a nightmare in such a case. Similarly, I use Cryptomator to store plain OpenDocument files (on arbitrary storage) rather than having encrypted OpenDocument file on a plain storage.
Using the FileProvider-Framework on iOS to specify a sync-target should be straight forward. This would not only enable Cryptomator-support but also other less common Cloud storage (that also integrates into the FileProvider-Framework).
I'm not familiar with the limitations and command line operation of iOS, but in Linux, you can copy a Joplin profile and its notes into a Cryptomator vault, and then open it with this command: Joplin-Vx.x.x.AppImage --profile /my/vault/Joplin/joplin-desktop
I'd be surprised if a variant of this command isn't available and working in iOS - see the command manpage. Having said that, you may have difficulty with permissions (as per the thread you cited). Perhaps someone more experienced than I can clarify.