Visible crew/equipment: Immediately after the scene where they are removing chairs from the launch facility and installing electronic relays, there is a panning close-up shot of the WOPR. When the camera reaches the end of the WOPR, there appears to be red fabric to the left of the WOPR that moves slightly before the scene ends. It looks like the back of someone's shirt who is sitting on the floor next to the WOPR. Perhaps this is the crew member operating the Apple II that controls the lights on the WOPR? (00:23:13)
Visible crew/equipment: When the FBI van pulls up in front of the 7-11 to take Broderick away, lights and other rigging are reflected in the van.
Answer: While merely speculation, the WOPR is not alive and knows only what it's been programmed to do. It would have no concept of life or death, and as such would see no difference between the simulation and the real thing. That being said, an easy way to make it see the difference would be to program it to not waste physical resources. It would then see the use of all its actual warheads as less desirable.