A global shortcut was available at one point to show/hide Joplin. But I had to remove it again, because the shortcut I used was used by a random user under Linux.
We then decided to wait until we had the shortcut system in place, but haven't added global shortcuts yet.
At one point there should be a separate section in the shortcut editor for global shortcuts.
I do like your idea, but I am afraid it does not fit the scope of GSoC this year. Or at least parts of it, since the global shortcuts and commandline args would have to be added to the core code.