For the past few months, it seemed like GitHub wasn’t sending me notification emails for all activity in my watched repositories. I was only getting a random subset of these emails, at most half of what it should have been. I eventually contacted GitHub’s support and they were immediately able to help me. They told me that they send a certain portion of their notifications not directly, but via a third-party service (judging from the message headers, it’s SendGrid).
This third-party service had apprently added me to their suppression list because one email they sent to me months ago had been hard-bounced. There probably was some malfunction on our email server at the time that caused this. I understand why SendGrid does this, but silently discarding any emails GitHub asked them to deliver to me is bad. Really, they should have notified GitHub, which then should have either emailed me at one of the other addresses in my profile or shown a big banner after I log in the next time, asking me to re-confirm my email address to clear the block.
So if this ever happens to you and you’re getting fewer GitHub notification emails than you should be: just email their support and ask them to check. I should have done this sooner, but it really wasn’t clear to me whom to blame (it could just as well have been our mail server’s fault).