I can see that it would be helpful to have some form of visual indicator that a file has been hooked. This hasn’t been a big issue for me so far because I primarily use Hook to connect files with my OneNote daily diary (basically a page a day in OneNote in which I record the details of the meetings and other work) or in DEVONthink. I use Hook links so extensively I just assume things are linked.
Still I have done some thinking about solutions. My first was to create a TextExpander snippet I can use to add the text “HOOKED” to the file (perhaps in the footer). I also have a snippet I use to create file names in a standard format. It includes an option to mark a file as “hooked” as part of its file name. I assume there are ways to further automate these measures via Apple Script, Keyboard Maestro, etc., but that is beyond my competency. I hope that helps.