I'd argue that Hipchat had the exact opposite problem with notifications. It was _too_ aggressive about notifying everywhere.
I've had many times where I was looking at a DM room with someone in Hipchat, with the window focused, and it was still sending me emails with every message from them like I was AFK. This is especially common on the mobile apps, both Android and iOS. I'd often be chatting on my phone at lunch, and come back to my computer to find 50-100 emails of every reply I'd gotten in Hipchat.
I've had many times where I was looking at a DM room with someone in Hipchat, with the window focused, and it was still sending me emails with every message from them like I was AFK. This is especially common on the mobile apps, both Android and iOS. I'd often be chatting on my phone at lunch, and come back to my computer to find 50-100 emails of every reply I'd gotten in Hipchat.