So Google says 'we will play the game just like everyone else' and not report to you organic search terms coming from SSL (even though we have access to the data), but we also have a product (webmaster tools) that we can show you who is searching for what to get to your site, albeit slightly more obfuscated? It certainly sounds like a win for end users, not really sure it helps webmasters trying to see inbound search terms though. It sounds like it makes people have to put a little more value on the stats that Google provides via webmaster tools.
If referrers from HTTPS pages were sent to HTTP pages by browsers anyone sniffing the connection would know the URL the user visited. For a search engine, this would make SSL pretty useless as the main thing worth encrypting is search queries and people usually end up clicking links to non-SSL pages.
I presume they're working around it for ads and (telling webmasters the user is coming from Google) by sending the user through a HTTP page before they reach the result (like DuckDuckGo does, but for the opposite reason).