It would be nice to know which case(s). None of the side panel fans on my cases rattles. There again I have 200 mm fans.
It's not the 200mm, but how much it flexes when it switches, how much the side panel can flex when that happens, how secure the side panel is to the case, and with a solid connection to the case (can't rattle), how much the case can deaden or dampen the pulses (also, a window adds another set of joints that can either help or hurt the situation). If it's not a problem, it's not, and that's fine. If it is, just not using the side panel fan(s) is typically the easiest and best solution. It shoudn't be an issue with a Corsair 400R or 500R, being that they're kind of made for that, and it's typically not an issue with the heavier Fractal Design cases, either, FI.