I just noticed that I got a "you have mail" indicator in my message box but there are no new messages. I'm assuming that this is related to the change here. Is it intended that replies are hidden even within inboxes or is that a bug? If not a bug it seems excessive and given a karma penalty redundant. Not that I especially mind either way but if you are going to hide messages from the inbox you need to also hide the 'new message' indicator for invisible messages.
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.
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.