They did not prove that Thomas Jefferson was the daddy beyond a reasonable doubt. They proved a Jefferson was the daddy. And there were a few amorous relatives around at the time who could also have fathered the Hemings' children.
I believe that T. Jefferson was the father, but that's just my feeling after visiting Monticello and reading a bit on the subject. My favorite professor, Forrest McDonald, believes T. did not father any of Sally Hemings' children. And he can't stand Jefferson! Jefferson was executor of several wills of slaveowners. It was the will of these folks that their slaves be freed upon their (the slaveowners) deaths. Jefferson did not free those slaves. His will provided that select slaves be freed upon his death.
you are correct---I was not strictly correct. Someone closely related to Jefferson may have been the father, but considering that it was an "open secret" at the time, I would conclude that it is more than reasonable that Thomas Jefferson had illegitimate children.