This probably indicates a dark pattern at work ( http://darkpatterns.org/ ) - it was presented as a quick, default and normal action and/or of little consequence, when actually it's quite invasive.
You said that Linkedin would "scan your contacts to see if those people are on LinkedIn" and this is likely what it is presented as, but actually that information might be retained indefinitely and may be used for other purposes that are thought up later. But hey, it's just metadata, right?
The LinkedIn Android App will periodically ask to scan your Google+ contacts for people you might know on LinkedIn, so if you've ever used that you could have leaked contacts to them that way.
I wasn't quite so security-conscious a few years ago.