Your intended point about pigeonholes can sometimes backfire within the context of email. Consider a Gmail user who sends a query to a number of different recipients, expecting unique replies from each. Gmail, because of the like headers, will group all of the responses into the parent conversation. Let's say the users tags the first response with a label corresponding to that sender, and then the second response comes in. At this point, the user is at an "oh shit" moment, finally comprehending the implications of Google's labeling of conversations rather than individual messages.

You need to be able to specify both parent and child tags to be able to facilitate search and give users something that isn't too confusing re: organization.