No, parents are both Japanese. His mom's family was a lineage of Onmyodo mystics which was the Japanese branch of Taoism and his dad was a Shugendo shaman, which is an old pre-shinto religion native to Japan. The point that was by being from two parents of different Japanese specific religions, and then marrying Anna, who was a Shinto priestess, Yoh would be the intersecting point of all of Japan's major religions. It's also why Ren and Horohoro were designed as rivals the way they were: Taoism-vs-Onmyodo, and the Ainu are another faith unique to Japan, but the Ainu never really integrated into the central Japanese identity after their ethnic identity got outlawed. It's kind of surprising there was never a Ryukyuan team member.
The Native American thing just came from Hao, because Hao was reincarnated from a previous life where he was part of the Patch tribe. Native American Hao isn't directly related to Yoh by blood, Onymo Hao was though. Native American Hao IS related to Silva, though. So when Alumi was made Hana's love interest in Flower, if they'd ever had a kid, it'd be the uniting of both Hao's bloodlines.