Equations aren't nature. They are descriptions of nature. Or, to put another way, if you take it as an axiom that those equations are real, then you are already assuming you are not in a simulation (at least not in a simulation that cannot handle such equations with precision).
In nature, we can't really tell if the equations we've concocted correspond with nature exactly. We can just make measurements and say that they match he theory to some degree of accuracy. We can never reach a point where we measure an
actual pi anywhere, because all our measurements are imprecise. As an analogy, take this shape:
What is the ratio of it's circumference to its radius? No, it's not two times pi, it's four. Because the image consists of pixels and if you look closely enough, it's not an ideal circle. Same might be true if we live in an elaborate simulation... the equations and wave forms look like they contain pi, but if we "zoom in" close enough, we'd find out that they are in fact just a close approximation.