Thank you for voicing this request, @katie_v .
There’s a General Preferences checkbox
Apply "Hook" Finder tags to files when linking them. But of course the tag is only visible from Finder, and then only if Finder tags are exposed which is a Finder option. In my usage I find that handles the file case relatively well, although Hook does not yet do dependency maintenance (if you duplicate the file it will retain the Finder tag). However, we plan to provide an option to remove the tag from files that are not linked.
We’ve heard from a number of users that it would be helpful to provide other visual cues, perhaps the most obvious one, which we’ve had in our internal issue tracker since well before launch, is for Hook’s menu bar icon to change state as a function of whether the selected item is linked; it would need to be a configurable preference. There are several complexities there (e.g., when should Hook poll, macOS warnings, etc), but it is on our radar and I appreciate your raising the issue.
Hook 1.2 (coming soon) and 1.3 will have significant UX enhancements, though not this one.