If we can operate submarines and aircraft carriers with nuclear, there is no reason why container ships and other cargo ships can't be nuclear powered. We could decarbonize the seas very effectively. It's not done simply because it is more profitable to use oil. 
What's the point? The point of nuclear reactors on marine vessels is to never have to refill. That isn't a concern on merchant ships at all. (Merchant ships ferrying cargo from port to port always have opportunity to refill.)