I've done the cargo ship upgrade, but it hasn't given me the option to actually build any ships. Any idea what I need to do?
If you're only looking in the bottom left list then you're not going to see things that you haven't built at least one of.
To build the first one you need to go to the Workshop tab and create it from the big buttons that make one at a time. After that you should be able to make in batches in the bottom left like everything else.
From the Wiki:
Cargo Ships are unlocked by the 'Navigation' technology. They increase harbor capacity, and can be used to discover new civilizations. They improve the chances of getting certain rare resources.
So you'll need to unlock the Navigation technology. Then you are able to buy them through the workshop.