AI Ships dont have any fuel limitations.
As to the Port to Port routine I counldn't agree more, and it is sort of possible on some ports. Those ports that have an enterance/exit thats easily transited can be used. All the ships need do it be told whilst in port to make steam for ˝knot. So as they enter the port to all intents they are moving so slow that to us they look docked. They would then slowly go through the port, exit out, pick up speed and do it all over again at the other end. The Start Nav point would be well out to sea and so would the End Nav. Then loop from End Nav to Start Nav and the ships will do this till the cows come home or get sunk, whichever comes first.