The first thing that came to my mind was the idiocy of stamping the Indian visa in a Pakistani passport, even if the applicant was a U.S. citizen. On the second thought, it's not all that silly.
1. Pakistan allows dual citizenship. There is no way for India to know whether an applicant who is a U.S. citizen is concurrently also a Pakistani citizen.
2. Once a Pakistani passport is presented, stamping the visa on it ensures that the person is unable to "hide" their Pakistani citizenship while entering India.
It makes it inconvenient for the traveller through. For example while checking in for their flight in the U.S., they have to show their Pakistani passport to the check-in staff in order to establish hat they have a visa to India.
If a dual US/Pak or U,K./Pak citizen of dual nationality intends to enter India for purposes of terrorism (instead of tourism), they do not even have to bring up their Pakistani citizenship. Moreover, terrorist hardly needs a visa to enter India.