We didn’t see the Wolf 359 ships again because they sucked. They were never screen ready, and I say that as someone who’s featuring a few of them in my thread Starships of the Galaxy Era. It would have been nice if they had the time and budget to give them the full service, not only installing lights but also addressing countless esthetic issues. There’s not a single ship theat didn’t need an extensive refit to play as a Hero Ship.
The Nebula class filming model was quite different from the study model used for BoBW. If any of the other designs had been given fully-fledged filming models, they would probably have looked different as well.
Given the completely hideous/senseless models they used in the background shots hovering over DS9 during the Dominion War, I think it’s obvious that they just slap together whatever parts they have lying around at the time. Like they did for 359 at its time.
There were two entirely different rationales for the Wolf 359 ships and the DS9 kitbashes, the main fact being that the former models were not built specifically for BoBW, but were originally 'study models' built by a contracted professional model maker to show that components of the Galaxy class could be rearranged to create new ship designs in an effort to convince the producers to budget for new filming models instead of constantly reusing the TOS movie models. They were used for BoBW because they were available.
The DS9 kitbashes, on the other hand, were hastily-built concoctions by members of the production staff, out of multiple types of kits without regard for scale or era, and were never meant to be scrutinized up close.