It had nothing to do with Yubikey. Mt.Gox implemented time based 2FA (think google authenticator) via Yubikey. The fact that Mt.Gox subsequently imploded had nothing to do with Yubikey and seems almost entirely to be based around a poor implementation with regards to handling bitcoin transactions combined with insider fraud.
Public disclosure, I lost ~$700 to Mt.Gox, a tiny amount compared to some, mostly I was just trying to cash out a couple coins at the height of the bubble. I'm not terribly upset over it, although it would have been nice to see that $700 in my account, or at least get my 2 coins back.
The prototype I've seen requires that you tap it, which is a major step forward. And I believe that the spec allows it to show something like "google.com" if it had a screen.
I think its pretty obvious that anything without a USB connection this probably won't work (maybe usb otg), but would 2FA still be used as a fall back ?