There was a famous black Samurai named Yasuke. The Ainu resided in the North and trade with various nations, most likely also produced some offspring from liaisons. But for the most part Japan was ethnically and racially pretty homogeneous. There are numerous cases of white traders and skilled artisans being persuaded to settle in Japan for various reasons. My guess is Shogun is extremely loosely based on William Adams.

William Adams: William Adams, an Englishman, holds the distinction of being the first white man to become a samurai. During the pre-16th century, samurai were skilled warriors akin to the knights of medieval Europe. However, by the 16th century, their role evolved to include managing land and people as political leaders. Adams arrived in Japan as a navigator and became a trusted advisor to Tokugawa Ieyasu, the founder of the Tokugawa shogunate.