I just tested this in a normal Japanese markdown page in Hugo, and it renders fine as is. I just pasted in the <ruby>茶<rp>(</rp><rt>ちゃ</rt><rp>)</rp><ruby> like a span, to test, and it works fine mixed in there. It did not appear to disrupt the markdown processing.
Edit: one thing that does not look good is, when you mix in a kanji character like this to English, the line height is effected and the page looks kind of messy. Adding ruby makes it worse. On an all-Japanese page, it’s probably not as much of a problem.