Not even close to all -- Navy watches rotate every four hours at sea. The collision occurred during the midwatch (midnight to 4AM). There would have been multiple people standing watches in engineering spaces, CIC (Combat Information Center), and on the bridge. I'd expect that about 1/4 of the crew would have been awake and on their stations at the time of the collision.
Track any ship you want!!
http://www.marinetraffic.com/en/ais/home/centerx:135.5/centery:31.8/zoom:6