Yes, we do know of such people. There were several ways by which Japanese came to Europe at this time. One is through slavery: in the second half of the 16th century, the Portuguese captured many Japanese as slaves, a practice which would eventually be regulated by the Jesuits, ineffectively banned several times, and finally stopped around 1600. In 1604, King Philip III ordered all Japanese slaves in Portugal to be freed (he had to issue the order twice because slaveholders tended to ignore such orders).

Another is through religion. In 1582, four young Christian samurai were taken across the world to Catholic Europe to meet with religious leaders and fundraise for the Japanese mission, a trip known as the Tenshō embassy. Unlike the slaves, the Christian samurai were never intended to permanently stay in Europe. When they returned to Japan Christianity was starting to be persecuted by the shogunate, and they all met unique but unfortunate fates.

I have not read "Isaak" but it sounds like it describes a fictional third route, extending the journey of Japanese merchants all the way to Europe. This references the "red seal ships" which sailed between 1600 and 1635, much closer to the timeline of the Thirty Years War. There were hundreds of red seal ships which sailed to Southeast Asia for trade. Most of them landed further north, in places like the Philippines and Thailand, but Jakarta may be famous to the manga author due to the story of the Jagatara-bumi, letters sent home to Japan from Japanese women stranded in Jakarta after 1635. These letters are known for being wistful and poetic.

While there is no record of a Japanese merchant coming all the way to Europe (it would have been a risky and unprofitable venture), there is the individual story of Tenjiku Tokubei, who rode on a red seal ship all the way to India in 1627 and visited various places there, so the fictional character of Isaak is not beyond belief. There are also, of course, dozens of Catholic missionaries who made the reverse journey at that time and lived in Japan for many years, some of them even concealing themselves in the homes of believers for up to a decade after missionary work was made a capital offense, so the passion to resettle oneself in a foreign land certainly existed at that time. It would have been more realistic to write Isaak as a freed slave, but I suppose this is much less romantic.

edit: I glanced at the manga and saw that Isaak is supposed to be a mercenary brought from Hirado. This references yet another type of seaborne travel of this time: masterless samurai were employed by the Sultanate of Brunei in a attempt to capture Batavia (Jakarta) from the Dutch. Another group of samurai mercenaries were offered to the Spanish army in Manila for use in an attack on China, but this was actually a trick by Japanese Christians plotting together with Bruneians to overthrow the Spanish colonizers. None of these guys came all the way to Europe, but again, it's not an inconceivable backstory for a fictional character.

The manga portrays ordinary farmers in the HRE as being aware of Japan, Hirado, etc., but I highly doubt this would have been the case. It is a useful plot device, though.

Sources

Broomhall, Susan. "Moving Objects: Reading the Emotions of Japanese Christian Exiles in Batavia". 2018.

Cooper, Michael. The Japanese Mission to Europe, 1582–1590: The Journey of Four Samurai Boys Through Portugal, Spain and Italy (Folkestone: Global Oriental, 2005).

De Sousa, Lucio. The Portuguese Slave Trade in Early Modern Japan: Merchants, Jesuits, and Japanese, Chinese and Korean Slaves (2019)

Japanese Christian-Bruneian conspiracy references an unpublished paper of my own, currently seeking an appropriate forum for it