The should not be a problem determining if any of the Duke students is the father, not that this is a real possibility.
The birth certificate should become a public record. The question is, when will it be available? Will Nifong try to get a court order keeping it secret/sealed so the suspicion over the boys continues?
If Mangum puts "unknown" as the father on the birth certificate, and Nifong never comes out and states one of the boys is the father, can the defense compel genetic testing? I seriously doubt it. There's the rub.