Actually, detecting brain activity in an MRI requires long aquisition times. Around 30 seconds per answer at least (which is the duration used in this study AFAIK). That means that a single "yes" (imagining you're playing tennis) or "no" (imagining you're walking in your house) requires 30 seconds of sustained attention.
This patient is obviously severely brain damaged.
If you've ever seen a person recovering from brain trauma, you'll know that their ability to focus is usually minimal. Answering questions for this patient may very well have been exhausting. This means that out of the other 22 patients in the study, some may be conscious but unable to cooperate long enough for the mnesic trace to be recorded.
Regarding other signs of activity, you can't detect random activity using fMRI. I haven't read this paper so I don't know the details (I'm only familiar with previous studies done by this team), but regarding heart rate, blod presure, etc, the brain damage may prevent it from occurring too.
Since he was only able to produce yes and no ansers using a contrieved process, he was of course unable to produce any other message.
He's definitely conscious.