I can’t be certain, but I think that it searches all libraries each user has access to, not the entire server. So if you want results to be omitted from a search, you need to use an account that doesn’t have that library available… At least that’s what I remember from testing a limited access user account…
Or am I misunderstanding the question? As an Administrator, I wouldn’t want anything omitted from my personal search results, however, my users (kids, friends, family) I wouldn’t want them to be able to see some of my libraries, so I just don’t give access to them, and as far as I am aware, when they search, those hidden libraries do not come up…