It helps with orientation. This is especially true if you are flying high and far away at night. Unless you have the entire plane lighted up (wings, rudder, canopy, fuselage, elevator, etc), you are soley relying on the lights for orientation.
When you only have the top and bottom differentiated by a different color, you will be able to tell top from bottom, but it is often very difficult to determine which way the plane is flying. Your mind plays tricks on you in the dark.
Here is a wing I fly at night. It has yellow leds in the shape of a V on top...and blue leds in a V on the bottom. You would think that with those colors...shaped into a V...that top/bottom and front/back would be easily discernable. Nope. Sometimes it is coming straight at me and my mind inverts the V. To compensate, I added two small strips of red leds next to the motor facing backwards (like afterburners). It makes a big difference. The same goes for different colored leds on the wings or tips. They help you determine the direction of the plane.