I thought the later years of Voyager had some odd/weird ship designs, where they let the CGI go in different directions. Overall, you're right. Most of the designs stick to a basic layout. I think they do that because the design language makes it easy for the audience to understand what's happening. If you watch enough Star Trek, you know that an explosion on a ship's nacelle probably means the warp drive is not gonna work for a while. Where if you make the design too weird, then the audience is either wondering what's going on or you have to do an exposition dump where you explain that the weird green blob moving towards the Enterprise was fired by the alien's technobabble launcher that is a technobabble technobabble.
Vger is probably the weirdest design Star Trek has ever done. You definitely get a sense of scale with it, and the Enterprise looks so dwarfed inside it.