It was only enslaved people that were counted at 3/5ths. Free blacks were counted as a whole person.

From Wikipedia:

Although the three-fifths clause was not formally repealed, it was effectively removed from the Constitution. In the words of the Supreme Court in Elk v. Wilkins, Section 2 "abrogated so much of the corresponding clause of the original Constitution as counted only three-fifths of such persons [slaves]."

So it's technically still in there, but moot with slavery being banned.