I'm posting this as an answer as this change worries me a great deal.
Not the fact that it happened, but how it happened.
Someone tweeted a complaint on Twitter about HNQ and didn't explicitly ask for anything to happen. This happened at 11:39pm (UTC).
40 minutes later, an SE developer tweeted back stating "Yes I agree, I've pushed a change to remove that site from the HNQ".
So, there's been a change to the site's behaviour in 40 minutes based on an external tweet.
If someone in my team pushed out a live change in that kind of time, they'd be hauled up in front of management and asked why the hell they were bypassing the change process.
Was this change discussed? Were the moderators of IPS informed up front? Or is this (as it seems to be), a rogue developer pushing changes out?