It happens in the same way that I'm making this reply 6 months after your post. This isn't actually explained well in the game but you also need land connection between your capital and your ports and you will be able to have access to all the sea routes provided by the ports, as opposed to just your capital (the game only refers to ports in your capital province or theirs as being available or not but in practice ports in other provinces also contribute, as long as there is land connection).

Remember that you need to have a land connection with your capital in order to trade by land. it's possible to deny Buddhist clans access to incense, preventing them from getting too powerful monks, also silk (archers IIIR) and cotton (top yari line IIRC) come from only one source being the respective node-horses and iron are harder to deny, as they can be found in provinces too). If you have the nodes, trade with everybody you can unless you really know what you're doing in denying a certain clan the access to certain strategic goods, if you're able to pull it off (e.g. The optimal investment return is probably around 5 trade ships per node but income does increase up until 10, I believe, so it does pay to have more (your investment return is worse but your income still higher than when you have 5 ships there). Just be warned that pirates can appear, so it's good to have a nanban ship somewhere in range to clean up.

2K A Total War Saga: Thrones of Britannia.

844 A Total War Saga: Fall of the Samurai.

Trade ships shogun 2