The Japanese Red Seal Ships were commissioned around the end of the 16th century. Essentially, these red seals were signed off by Hideyoshi or Tokugawa, basically giving permission for these armed ships to go trade, and that anybody attempting to pirate this trade would be very sorry. These ships went to southeastern trade ports-the Philippines, Malaya, Indonesia, Thailand, Vietnam, and so forth. This was a pretty big deal, to the point where there were samurai enclaves in Thailand, and many Japanese Christians ended up emigrating to the Philippines after the Japanese crackdown on Christianity.

However, IIRC Shogun 2 starts in 1560, which is way before the Red Seal system was implemented.