I had noticed the much higher frequency of the first structure a long time ago, and your search confirmed my guess, because I don't remember many (or in fact any) instances of hearing "isn't" and "aren't" in American movies. It's (almost) always like this:
He's not there. / They're not here.
Is he a student? No, he's not.
Are they going somewhere? No, they're not.
My guess is that it's because "isn't" and "aren't" take a little more energy to pronounce than "'s not" and "'re not". The latter two are easier to prnounce. You can try it for yourself and make a comparison.