I would be perfectly happy to receive a popup that an automation had just run. Also, Apple has been pushing for self-adjusting notification preferences. Imagine a popup like:
"The shortcut 'Foo' wants to run. Do you want to allow it?
- Never
- Not this time
- Run once
- Always"
Put an icon next to each shortcut showing whether it's always (or never) allowed, and it seems like the problem would be largely solved without asking much from the end user.