Kon's had a number of close friends, such as Dr. Serling Roquette, who have worked on his DNA, like when he got messed up during and after Sins of Youth, and various other times his clone nature has come back to bite him in the ass. I would think they would mention it at some point. And Kryptonian DNA was established as very different from Human (to the point that originally no one could make any sense of Kryptonian DNA), and I bet even a bloodtest would turn up something unusual. "All right Kon, your blood type is... F-? What?" "Wow, I knew I was bad in school, but I never thought I could fail a blood test."
Batman could have gotten a sample while Kon would doing his punishment, perhaps. You know, just in case.