Highly doubtful. Any change should be inconsequential. The laws of physics dictate the conventional frequencies are for the most part “ground wave” dependent. (So if you are differentiating between the sphere layers, it’s not a concern.) But the scope of your question is broad in nature. Define what you mean by atmospheric conditions. Band openings (Skip)? Or barometric and temp changes?
I would think the physical location of the scanner should have more to do with a decision to use a filter setting than atmospheric conditions. That’s why I did not attempt to improve reception by using filter settings on the SDS200 I have mounted in my truck. I did try filter settings on the SDS200 at home, saw no difference and chose not to use them. (I am fortunate to be one of those people who receive all that I am interested in without any interference, simulcast, etc.) But I never considered atmospherics as a factor when choosing a filter.