Presumably, Luke knows some galactic history and what clones looked like? If Ben isn’t a clone and he fought in the CW, he can’t be a Trade Federation guy either, as they were mostly non human.

Also, Ben is probably confident he knows Luke well enough to tell that he’s no Empire loving snitch. Even though Biggs only confided in Luke his plans to join the Rebellion, we don’t see evidence the local population likes the Empire all that much. Only one guy even bothered finding the nearest sand trooper after that little disturbance in the cantina.

Interestingly enough, there was speculation back in the 80’s that Obi Wan was a clone designation, possibly derived from OB1.