Probably needs some adjustment or moderator intervention in the near term. I just tried a moment ago; you can still submit a pages.github.com URL and HN will mark the domain as github.com, but it will redirect to github.io when you follow the link.
Indeed, it's not like there are an endless number of common subdomains which don't convey much information. "www" is one, "blog" is another. That's about it.
The problem wasn't anticipated, and the fix has been to enable showing subdomains on only on certain domains, mainly blog hosts like wordpress, blogspot, tumblr.
