I disagree somewhat- hiding new messages from the inbox is a bad idea. People should be able to know when new messages have been made to them. The primary advantage that would occur here is that people who browse using Recent Comments won't see them. This doesn't accomplish anything.
This is indeed a bug; the feature spec said not to hide from inbox.
I just found out that a new website feature was implemented 2 days ago. If a comment is voted to -4 or below, it and all replies and downstream comments from it will be hidden from Recent Comments, and further replies in that subthread will incur 5 karma points penalty. The hiding, but not karma penalty, applies retroactively to comments in that subthread posted before the -4 vote.
This seems to be worth a discussion post since most people are probably still voting things to below -3 without knowing the new consequences of doing so.