NES does not allow controller ports to generate interrupts... so when you press the trigger, the game whitens up the screen, and sees if gun reacts to it then it leaves the object you shoot black, and when gun sees nothing then the game knows you hit the target. This is just one method, and this method is not fooled by the lightbulb trick.
SMS and MD allow controller port to generate in interrupt and the VDP provides pixel coordinates also and this makes the gun stuff more flexible.
All the light sense based guns work exactly the same... if they see light they react by pulling up/down a signal... its up to the HW or software to deal with the signal.

Death To MP3, 
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