"They don't have to deal with unpredictable atmosphere"
Well, no, but they do have to deal with an atmosphere that has, until they get to it, only been theorized about, never observed - which is not the case for the atmosphere above New York.
There have been precisely four spacecraft that have gone anywhere near so far out as New Horizons, and they are between them the source for the majority of data we have about the atmosphere in the outer solar system. One of them discovered an anomalous acceleration effect that confused scientists for decades (and which, while it turns out not to have been externally caused, certainly left scientists wondering for a while whether their model for the solar wind was accurate). Of those that we believe have passed through the termination shock of the solar atmosphere, none have yet returned much accurate information, so we actually don't know much about the conditions there. I don't mean to say that these effects have meaningfully impacted navigation for deep space probes, but more these are genuine voyages of discovery - where they're going is predictable but until they get there we really don't necessarily know whether our predictions will be accurate.
Well, no, but they do have to deal with an atmosphere that has, until they get to it, only been theorized about, never observed - which is not the case for the atmosphere above New York.
There have been precisely four spacecraft that have gone anywhere near so far out as New Horizons, and they are between them the source for the majority of data we have about the atmosphere in the outer solar system. One of them discovered an anomalous acceleration effect that confused scientists for decades (and which, while it turns out not to have been externally caused, certainly left scientists wondering for a while whether their model for the solar wind was accurate). Of those that we believe have passed through the termination shock of the solar atmosphere, none have yet returned much accurate information, so we actually don't know much about the conditions there. I don't mean to say that these effects have meaningfully impacted navigation for deep space probes, but more these are genuine voyages of discovery - where they're going is predictable but until they get there we really don't necessarily know whether our predictions will be accurate.