The Finder is most definitely NOT a universal tagging system. There are Finder tags yes, but they can only be applied to documents that Finder accesses. You cannot tag emails, Apple Notes, Apple Reminders, Message chats, or any other objects that are contained within a database system and not held in the Finder in some way.
Everyone has different ways of conceptualizing their work space and therefore different needs. Through a universal tagging system I can accomplish all of what you describe in an efficient manner, using a standardized set of tags and keyboard shortcuts. Each object is described by tags of various categories, including descriptive of what the file pertains to, but also status tags such as active, task, waiting on, etc.
Regardless of this, what I think the incredible power (and potential) of Hook is that the concept of it is adaptable to many, many different ways of approaching organization and structure for a wide variety of people. But that power for now isn’t fully accessible as you aptly describe. We need a way to visualize all the connections that Hook contains beyond what is visible in the current manifestation. Sounds like there is a roadmap that will address these issues that will become apparent over time.