I don't think you can change the distance of the shields from the model. You might be able to do something by editing the graphic files, but the easiest thing to do would be to edit the models. The M6 editor would be perfect for this. There is some element of the model it can't edit, so the game engine doesn't know the ship is smaller. For example, if you took a K'vort model and tried to resize it into a B'rel, the shields would be huge with a tiny little ship.
What you might do is make the model bigger in Milkshape, which should cause the shields to scale up with it, then shrink it back down to the original size in M6, which will only make it look smaller while leaving some invisible element still enlarged so the shields don't overlap the ship.