Small Scale Military Headquarters

I noticed that the rack (for lack of a better term) which holds the missiles has clear plastic ends at the rear, while the rest is painted. Are the clear ends supposed to be lights?

The missile rack, or rails, in that configuration is called a catamaran. The clear ends are lights. I'm not sure of their purpose, but it's probably for identification. I've seen green ones before on other planes, and one catamaran set that had green and red. I always thought it was strange that 21C chose that missile configuration. It was actually rarely used on F-104's. You usually see them with sidewinders on the wingtips, and other missiles slung under the wings, which would have been a better, more cool looking choice for a toy. But anyway, I've noticed an interesting tidbit here: All of 21C's F-104 catamarans had clear ones; the Boelcke F-104 from JSI has blue.

Thank you for the explanation, zodiac!

You're welcome.