In that case the ship is almost certainly battened down for the second hit with nobody on the deck and blast shutters in place on the bridge, so it's unlikely they'd be any further injuries at that point from the blast.
http://nuclearsecrecy.com/nukemap/?t...888cb2e3623787
Where was the ship departing from? My best guess is the ship would have been stern on to the first blast, and hit from the starboard by the second.
Also, once the first nuke hit, the Captain (or whoever is in charge if he was wounded) would likely order the maximum possible speed to get out into the ocean and away from a possible follow up warhead.