Everyone knows how software works. You have a program, and you give it to a computer, and the computer conforms itself to the program and instantiates all the rules and carries out the program's instructions. The universe works just the same way, only without the computer. -- the negation of the Simulation Hypothesis
Bell's Theorem says there cannot be local variables determining some phenomena. That raises the computational cost of simulating the universe, and shrinks the set of possible universes that could simulate ours, but does not preclude the universe being a simulation.