Yeah, the mixed scales of the components of some of those really hurt the eyes but, like you said, ships like the NO and Cheyenne do look reasonably well-balanced in their architecture.
Nothing beats the oddity of the never-filmed kithbash USS Trieste, though, which was said to have potentially been a member of the Merced class (an apocryphal claim). That thing makes most of the DS9 frankenfleet look majestic (all due respect to Mr. Dan Curry)!
The mixed scales didn't bother me that much. Star Trek has a LONG history of spacecraft of different sizes with the same dimensions (Starbase 74, Br'el and K'Vort class, Centaur parts etc.) It's more the composition. One top and bottom nacelle doesn't really look very good. Given that these ships were hastily prepared for a 2-second-long shot on non-HD TV's in the days before quality screen caps, and mostly burned beyond recognition to boot, I doubt TOO much concern for aesthetics was given.