Well, the Constitution says to count the "whole number of persons", not citizens.
As for the idea that they would have been deported, don't forget that at the time of the framing and for the first hundred years of the republic there was no such thing as an illegal alien.
We had open borders and everyone was welcome, so it makes sense that the framers would have wanted to count everyone.
At the time, yes. But when the Constitution was written, States were regulating immigration and it wasn’t a Federal responsibility, nor were the immigration laws that exist today (and ignored) in place. Including illegal invaders in the Census is akin to levying income taxes on bank robbery proceeds.