*1. ...Rama "solves" this with a sheer cliff on one side of the sea, against which the water sloshes...*

Answered by yourself

*2.The sea takes up space – nearly 20% in Rama's case – that could be dedicated to habitation, agriculture, and so on.*

Sure, but if you need the water, and humans do, then you gotta put it somewhere.

*3.The sea, especially if it occupies the circumference of the inner surface, is a barrier to all surface-based transportation.*

Unless there are bridges and vehicular transportation.

*4.If the primary purpose is water storage or recreation, then arguably numerous smaller and less obstructive lakes could do the same job with fewer or reduced downsides. In fact, smaller lakes could be even more effective (e.g.: if the goal is recreational coastline, ten lakes 1/10th the size of the sea would have more than three times the sea's coastline; water stored within the hull does not pose a flood risk).*

You might be right about smaller lakes in terms of storage, but then you have to find ways of containing those so they wont create the same problems you say the bigger body would have. IMO your trading one problem for a lot of little problems, with not much benefit.

*5.Water is less dense than the surface and sub-surface material it replaces, which could throw off the balance of the habitat and cause it to spin end-over-end.*

But surely a technology advanced enough to create all this in the first place has already accounted for that in numerous ways.

My two favorite benefits for you are:

A) Drinking water. They have to treat it before drinking it of course, but as I said, the water has to go somewhere. 

And B) Radiation shielding. To be sure, Rama didn't use its water for that purpose, but it could be used that way.

Good luck!