> Why assume the author of this system is even aware of us at all?
Think about why we simulate systems. There are two reasons that I can think of to do so. First, to exist inside of it, like a flight simulator or Minecraft. Second, to observe the emergent effects, like Conway's Game of Life. Assuming we're in a simulation, we'd have to assume that we're in the second kind of simulation. (Now that I think about it, what we term as deities could simply be alien 'players' of our universe game. Other examples of the first I can think of are ridiculously over-powered humans like Steve Jobs or John D. Rockefeller or Genghis Kahn.)
Assuming we're living in a simulation of the second type, it's the emergent properties of these that make them interesting. Emergence means you can't make a predictive mathematical model of what's going to happen. If what you're after is something you can predict mathematically, then you'd just do that with an algorithm rather than run a much more complicated simulation. We do do things like make computers in Minecraft, but the size and complexity and overall 'seriousness' of our universe sort of implies that that would have been a design goal for our world, rather than some cosmic two-year old's science project.
It would seem to me that if you have the power to simulate the universe then you could probably model quantum effects mathematically. I mean, we already do with the classical laws of physics, though obviously not to that level. I would think that life itself would eventually top the list of research priorities for our supernatural creators. I'm not saying they'd be interested exclusively in human-like intelligence, but they already had billions of years to study cosmic physics. Why keep the thing running once life starts evolving if that's all you're after? Ethical issues aside, it would have to seriously impact the performance of your simulation algorithm, the same way that sort of thing makes our own games more complex.