Can Jhin Legend ability play more than 12 runes with his passive?

No, you cannot exceed the maximum of 12 runes on the board using the ability of the Jhin Legend, Virtuoso.

According to RiftJudge FAQ #9949 (which addresses the interaction between the Jhin Legend and channeling runes), if you are already at the maximum of 12 runes, you cannot channel additional runes. If you attempt to channel, that portion of the effect simply fails to execute. Furthermore, channeling specifically refers to taking runes from your deck and placing them onto the board; it does not count as readying existing runes.