I don't remember Harada's performance/role being all that Tony worthy (and frankly, in theory, if it's isn't worthy of a win it doesn't really need to be nominated)...
Anika Noni Rose's role and performance of that role was much more worthy of a nom and win. Frankly I'm more surprised that we saw no nomination in that category for Veanne Cox or Chandra Wilson in Caroline or Change, both who gave amazing performances in layered and fairly large and notable featured/supporting roles too.
I was also pretty surprised when neither of the women of Assassins (Becky Anne Baker and Mary Catherine Garrison) were nominated for their fantastic performances.
Liz McCartney in Taboo not being nominated was also a surprise.
I did not see the critically bashed (besides Jackman) The Boys From Oz, though I wish I had, or the ignored Never Gonna Dance, so I can't speak to whether or not I think Beth Fowler, Isabel Keating or Karen Ziemba deserved their nominations that year, but I can say that Ann Harada is by no means the only standout or deserving featured actress in a musical who might have deserved a nom that year and didn't get one.