I have a slight preference towards hand-drawn backgrounds, but only because often if they're untouched they often clash hard against the style of the drawn characters. Even for rigid geometric shapes they give off a look of being... too perfect I guess? And also just at a much higher level of detail and graphical fidelity especially if the artist themselves didn't make the model. Like from experience I know if I'm drawing a high rise skyscraper in the background, I'm going to simplify the amount of detail the further into the background it goes. With 3D models though the detail is all there and just gets smaller the farther away something is so it can look... re: too perfect, or perhaps too real? idk.
The best compromise that I like seeing is like what darthmangoose described above where they provide a traceable base for the actual comic. Just by drawing over them, the artist's style and line quality shines through, but it's still much faster than drafting each element of the scene from scratch.
Another option (maybe, I suppose very dependent on what options the modeling softward has) is to try and find a way to render the model with a looser rendering style. The 3D modeling program that I use for work (Architectural modeling) has a variety of render styles, some of which are denoted by "Sketch". Those render with different contour line qualities that you can mess with to give a more pencil-y or pen and ink type of look to the building geometry. I think utilizing settings like those (if the program in question has them) would be preferable as well to just the generic thin lined 3D model look that I see... a lot in comics that use 3D backgrounds.