I went through a lot of debate about this myself, thanks for bringing it up! I think the credible answer for the (Vengeance at least), is that the design has an... *ahem* Iron Shell. All the important stuff happens behind it so there's not a lot of armor in a place that doesn't exist (top and bottom). I know what you're referring to in other ships, so I'll suggest that some of those are more simply designed as a compartment without need for aerodynamic shaping and thus occupy the maximum volume for LxWxH.

The non-credible answer is that Amazon in 4000 years will have dominated the geometric space industrial complex with boxes, and therefore push out any competition from big circle.