I think it is ok to appear for H-4 visa stamping w/ current documentation. In DS-160 form, there is a question asking whether the applicant has ever been known by a different name. There you can mention Latha as the other name.
If you update her name in your passport now, that would result in a new passport being issued. As her passport, and marriage certificate has Yamuna as the name, it should be fine. If asked, she can explain the situation to the VO.