Could you also please give us some idea of how your query or queries are constructed, and a brief idea of what indexes (if any) might be in play?   My intuitive sense is that “2 to 3 hour” run-times might be avoidable, and if that be the case it would make all the difference.

Otherwise, I think, the operative question would be how well your database servers could handle whatever-it-is that you are doing.   Particularly if your queries are resource intensive (and let us for the moment presume that they unfortunately must be), the question most-likely is going to be determined by just how many such queries your hardware and software is able to handle, not specifically “which database” is the specified target.   (“This or that database” might merely boil down to a choice between directories... functionally irrelevant.)