Think of it like how Apple's Photos works, particular the in-app Photos tab.
It's a chronological list of all your photos, but any that you've marked as "Hidden" (an option in the bottom row of the share sheet) don't appear there. You have to visit Albums > Hidden to see them.
Maybe we could even apply that idea here. In the settings area of each notebook (with options to keep offline, or add to shortcuts), there could be a "Hidden" toggle. If enabled, the notebook's contents don't appear in All Notes or search, only when viewing that notebook directly.