Real life answer: Because it is easier to film it that way.
- What's so difficult about hanging one model upside down and one the right way up?
--- for a start peices could fall off the model. Also it's a matter of look, while we intellectually know that space is 3D etc it'd still look odd.
Also, it probably makes docking procedures easier.
These are generally not cheap plastic model kits they used on the show, these models were very large and heavy, filled with delicate parts and electronics. These weren't exactly hung on fishing line either, each model has to be mounted on a special stand that allows the crew to manipulate it's orientation to the camera. Most models only had two or three mounting points, "ships of the week" often had even fewer, and it would take an entire crew to lift one of these models and move it to a different mounting point. Hence it was easier to film them all with the same side up. Another reason was that the models used in the original series had even less freedom of movement, so many models on that show were filmed right side up by neccesity. The crews of the later shows and movies may have been trying to emulate the feel of the TOS model shots.
Although this is speculation, I believe that within in deep space the ships align themselves to the galactic plane, with their dorsal side and the up with the north galactic pole, and their ventral side down with the south galactic pole. Then within a star system, they realign themselves to the palne and poles of the local primary star.
An alternative explanation is that when one ship approaches another, one adjusts to the other. This is supported by a scene from "Paradise Lost (Part 2)." When the Defiant and Lakota approach each other, we see the Lakota on the Defiant's view screen changing its alignment to match that of the Defiant's.