It sounds like the only thing requesting the 404`ed page was google bot, which I do not believe tells you the referrer. If this is true, then it would mean either that google does not clear their cache (which I doubt), or that the link exists somewhere on the net, but in a place where no human would find it. I've done some work with web crawlers, and it you fall into that type of hole alot more often than I would expect.
I removed a whole section from the site at the same time. Webmaster Tools shows the incoming links for every page in the section as other pages in that section. It's a whole loop of pages linking to each other and generating inbound links even though they all no longer exist and haven't for many months.
Yeah, Webmasters is reaally slow to update. Thankfully they offered a way to delete old pages. If they come back though, then it should show the source of the link.
