I can't imagine that this would be hard to do since, yes, functionally the boats and barges would be little more than floating mules and wagons. However, watercraft could possibly carry more with less work. (A small raft could conceivably hold several mules worth of goods, a barge could hold a few wagons worth of goods, and ocean-faring ships could hold more than you could ever want. A good load multiplier between mules, wagons, and their aquatic counterparts might be two or three, with the ship being able to hold three barges worth of stuff - six or nine wagons of goods.) This would be an even greater incentive to build on the water, especially on the coast where drinkable water and mining resources might be scarce. Another incentive might be speed - Since traveling over water is generally faster and less taxing than traveling over land, perhaps civilizations that trade via water could attempt to trade multiple times a year instead of once during a designated season?
-~*~- New Building - Pier:
Function:
Facilitates trade with watercraft.
Notes:
Can only be built over water with an adjacent walkable perimeter. (Such as a bridge or a constructed floor.) Brooks will only be accessible to rafts, rivers to barges and rafts, and deep oceans to ships and anything smaller. A feature for ship accessibility not unlike the wagon accessibility check for trade depots would be necessary. Watercraft traveling downstream or inland from the ocean will approach them (or visibly pass an inaccessible site) and dock at the pier before going on their merry way.
-~*~-
I'm almost totally certain that this has been thought of before but I'm putting it out there anyway.