Yes. All links show up in Google Webmaster Tools, but Google Webmaster Tools does not make any distinctions between incoming links that pass link popularity and incoming links that don't.
The links in GWT are a much fuller list than the results returned from the link: operator, but Google never said that the GWT link list is 100% complete, and it isn't. Neither does that list filter out links that are not passing PR - whether that's because of rel="nofollow" or because of an decision Google made.
So it looks like the guy has to analyze every link himself.
So the best would be just to get the list of links and parse pages and see which have / do not have nofollow.
By the way, Joost de Valk has written a pretty cool Greasemonkey Google Webmaster Tools Script to give you more information about those links.
Forum discussion continues at WebmasterWorld.