That is to ask, in the ports in which those missionaries and traders were acting, were there any outbreaks that occurred as a result of the Europeans presence?
Also - this might be its own question - Was Japan affected by the Black Death, and if so to what extent?
While it would be much better to wait for the answer from proper specialist in this field, I, though neither specialized in this era nor in this period, just make a brief notice of the situations in Sengoku and Edo Period Japan (Please delete this post if it does not meet the required academic standard of this subreddit).
Your question is actually quite interesting: Two diseases outbreaks in fact came to Early Modern Japan as a result of famous Columbian Exchange, but the known records of their outbreaks/ arrivals did not exactly corresponding with the arrival and activity of European missionaries and traders.
As for your additional question, in short answer, No. There is no known record of Y. pestis patients in Japan before the Meiji Restoration in 1868. The first record dates from 1899, and the last instance was in 1926 (Katow 2010: 43f.). The Mongols certainly attempted to invade Japan twice in 1274 and in 1281, but both attempts ended in failure, so the possible outbreaks of the Black Death in China in the 1330s and 1350s, mentioned by Abu-Lughod, did not apparently affect Japan. It is also worth noting that it was very difficult to identify the historical outbreak in pre-modern Eastern Asia like China and Japan due to their cremation burial practice, in contrast to Christian Europe. Thus, the microbiological studies that could identify the exact cause of the Black Death (see this thread) will unfortunately not work in this area also in future.
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