I can recommend Plagues and Peoples to anyone who wants to read more. But yes, theories about miasma, and about disease spreading via smells was certainly a thing, hence the classic plague doctor masks. However, there isn't a direct correlation there to hygiene, in fact I might suggest the opposite, that the cleaner people are the more noticeable smells might be. Anyway, this entire topic is really neither here nor there. Fantasy plagues would by needs by different anyway unless you're playing low-magic.