Are stories of flying saucers appearing just before outbreaks of deadly plague in the middle ages really true, and were these outbreaks caused deliberately by the aliens involved?

This is very much the case. There was much conjecture but there was also an intuitive awareness of a sinister interconnection that motivated the authors to seize on these observations not appreciated at the time, but only much, much later when someone from the modern perspective, understanding the microbial realm as a cause of disease and understanding the nature of the organisms responsible for the plague, could put two and two together and see a possible interconnection. This is what happened, that there was a purposeful introduction of Bubonic plague by extraterrestrials wanting to cause massive death among humans.