To shoot the ducks you point the Zapper at the ducks on your TV and pull the trigger. The trigger input is monitored by the game, when the trigger is pulled the gun is tested to ensure it’s detecting light, the next frame is rendered black, then in the frame after (or the next 2 frames after) a white target box is drawn where the duck is.

Demo of the target detection.

The black frame is used to ensure that the gun is pointed at the TV and not at another light source, the Zapper should register no light, if there is light then the gun is not pointed at the screen and a miss should be registered. For each of the next frame(s) the status of the gun is checked to see if there is light registered, if there is then the target corresponding to that frame registers as being hit.

https://beardypig.github.io/2015/12/11/nes-zapper-experiments-1/