Be gentle with me, because I can't figure this one out. If you don't want a link visible on your blog, why put it in the link manager?
Do hidden links still show up in Technorati and other link trackers?
That's the only reason I can think of why you'd want to go to the bother of entering a link... and then hiding it! So you get credit for linking to another site without actually showing the link on your blog.
Although I'm still unsure why anybody would want to do even that.