What is the ruling on the whispers that my sister experiences regarding creation, the universe, the afterlife, and eternity, and are these questions considered polytheism (shirk)?

The sister's anxiety and fear of shirk (associating partners with God) are evidence of the soundness of her heart and the strength of her faith. Satan's whispers are directed at those he has failed to lead astray. She should turn away from these whispers, for she will not be held accountable for those that overcome her. It is better for her to ask Allah for well-being, not for death. Among the things that will help her get rid of these whispers are: seeking Allah's help, sincerely turning to Him, and supplicating frequently.