What is the ruling on working in navigation on a ship that sometimes transports prohibited goods, and is it obligatory to investigate the goods, and does the sin fall only on the company?

There is no sin upon the sailor for his work on cargo ships because he is hired for a permissible job on a ship that mostly transports permissible goods. The one responsible for preventing prohibited goods is the owner of the ship or its manager. As for the sailor, he is required to advise the person in charge if he becomes aware of prohibited goods, but he is not obliged to search and investigate the nature of the goods, especially since his situation is one where the affliction has become widespread.