I think if the Vex could do this then we wouldn't be able to win. So obviously they can't simulate us. (Guardians)
If they can't simulate us then we aren't in a simulation. If we were in a simulation than there would be no reason why Atheon would be confined to the vault.
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They could be simulating real life situations, like testing out what would occur if a group of guardians invaded the VoG in reality, and there would be no reason to go out of their way to save Atheon if the guardians were about to kill him in the simulation, because they can just bring him back and run the simulation again
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If you think about it that's what the raid is..guardians going in to "kill" atheon..but he never really died it just resets.