What is the ruling regarding a ship's captain who carries a cargo of alcohol or pork, and how does he pray when he is at sea for a long time?

As long as the person is unaware of the existence of prohibited items on the ship, the basic principle remains, which is innocence. Prayer on the ship is possible, as one can face the Qibla and pray. If one fears harm from standing, it is permissible to pray sitting, and it is most likely permissible to shorten the prayer.