The only way it connects with other cities on the water is by the huge waterfalls and rapids near Ivarstead. In other words, the only place ships can travel to from Riften docks is to Ivarstead or the honey farm and back, and even if they did go to Ivarstead the ships would have to dock upstream so they didn't get caught in the rapids by the town. The Honey farm has a perfectly functional road and bridge that leads right to Riften, and if you think about the time and money it would take to build a dock between the two, it's far cheaper and just as fast to take the road.
So...why does Riften even have one of the biggest docks in Skyrim? The boats can't get to or from the docks to anywhere else of note, and the only way they could have gotten ships to Riften in the first place would be to build them there.
(Probably thinking to in depth about this, but it's been bugging me ever since I saw Riften

)