Google's Matt Cutts said in the ongoing Mozilla penalty discussion at Google Webmaster Help that Google will generally send the webmaster tools notification to both the non-WWW and WWW verified Google Webmaster Tools account.
Matt Cutts said the reason is because even though "that example.com and www.example.com are different hostnames and technically could be different sites, but in practice they're almost always the same." Since that is the case, Matt said they send it to both verified accounts in most cases. Matt wrote:
We wanted to avoid the case where a site owner verifies www.example.com and then misses out on a message about example.com. So when we send a message about example.com, we typically send it to the verified owners for both example.com and www.example.com, just so a site owner doesn't miss out on getting a message.
Not only that, Matt said Google will "continue to look at ways to make the messages more concrete and actionable though." As they have been, but sometimes more details but not full details can be less confusing than fewer details.
Forum discussion at Google Webmaster Help.