Airship trade would be an interesting concept in conquest and the upcoming multiplayer conquest, allow to trade goods for varying prices at different ports, you could also be able to hire AI privateers to hunt down enemy traders, or build your own. You could have different types of cargo hold depending on the ship. It could allow a variety of ships from huge floating east Indiaman to small and fast airship schooners.
You don't really have to go that far into the rabbit hole, but yes, Airship trading would be nice. To mitigate the micro-management of constantly moving in-between cities to perform trade, I would suggest including a Patrol/Trade Route command which makes ships constantly follow that path unless told otherwise.
This comes in a lot of different flavors. Considering the push for MP-CAMPAIGN, such a feature could be implemented automatically.
So instead of a Tech Bonus; you could receive a "Trade Perk" - and if paired with a corresponding "Trade Perk" (another city), then you receive the "Trade Bonus" automatically. "Trade Perks" could vary, would only be compatible in a handful of instances.
My original push on this suggested Modules, but those builds would be near-useless for multiplayer... and anyone who knows me, that would mean an additional version of every ship created (light armor to heavy armor + trade version). There's a lot of ways to approach it.
Perhaps simply make trade stores not available in multiplayer single battles? It would at least help limit some confusion, and God knows we already have that with the Coat of Arms not displaying bonuses in such a way the player thinks he can have multiple.