Bryce is a good 3D program, but generally I concentrate on top down maps. If I want to create an ornate rooftop, then I do that, but don't waste my time creating the building underneath the eaves - it will never be seen from a top down perspective. You can also place some rooftops at a higher elevation than surrounding buildings to imply taller buildings. Rather than creating raised roadways, as in your 3D rendering, my roads would be cut into the ground plane - a lower elevation than the ground surrounding the roads. I still might place a pavement, but a simple repeating texture of flagstone pavement on a flat polygon plane placed in the space between the ground plane and the cut streets. Your piers and bridge are fine.
Note when I say I use 3D to model detailed structures and complex objects, I am just creating the rooftop or complex object. I don't need to do the entire map in 3D. My normal techniques in creating any map doesn't change in that I rely on a vector drawing application to create 90% of the map. Only things like detailed rooftops, city walls, piers, and especially the ships might I spend the time of doing 3D work, everything else is done in my preferred mapping application. These days I never place texture maps on my 3D objects, I usually apply a flat 10% gray in the 3D program so the appropriate shadows are depicted. I export that as a JPG, import to my preferred application, where I apply semi-transparent layers of photo-image fills or fractal color mixes to accomplish a faster and easier way of finishing my 3D objects.
I only use 3D to create those details that are difficult to accomplish in other ways. As in any art composition, you don't need to perfectly replicate every realistic detail, you only need to include enough detail to convey that extra level of detail to make a remarkable final result. If your rooftops, trees, city walls and ships in the harbor are done in 3D, your overall map really pops, enhancing the existing map you created in Illustrator or Photoshop.