A year or so ago, I tried removing some internal links, but I failed to do this directly in the html. Rather, I simply deleted the links as I saw them in the design view (Dreamweaver). For some reason, the <a> portion of the links remained, and only the anchor text was deleted. This was a careless mistake on my part, but it raises an obvious question... were those being seen as hidden? I've done a sitewide search-and-replace to eliminate all occurrences (total of about 7, including a couple of outbound links, but mostly internal).
My thought is that they are seen as hidden, since all lynx browsers and fetching as Googlebot shows the link in the code. This is a lesson learned for me-- make sure the link is fully deleted by viewing the html.