My dad has applied for B2 Visa extension and his I-94 would expire by the time his case is processed. In case of denial, will his B2 be void? How will it affect his travel to US for the next time?

If your Father no longer has a valid visa to reenter the U.S., he must first obtain a valid visa to return. However, there is no requirement that he obtain a new Visa just because he sought an extension in the U.S. notwithstanding the outcome of that extension.