In the novel 'The Death and Life of Superman', it describes Superman as having considerably more chromosomes than a human, to the point where the scientists are amazed that he looks so human.
Interesting, particularly in light of Clone-Clark on L&C. If a scientist was researching and experimenting on human cloning to the point of being able to create one, I suspect they'd have to start from scratch when the got a hold of Kryptonian DNA!
As to the point of the fingerprints, I suspect we can all allow for any author's interpretation of the issue for the purposes of his/her story. Assuming he has fingerprints, Clark and Superman have both left them in a multitude of places. It would only take a motivated investigator to put the pieces together. It could certainly make for a good story!
