Perhaps a quantum probabilistic NOT gate requires the columns to add up to 1, but it's certainly not a general requirement of any physical device that imperfectly implements a NOT gate.
Consider the following probability matrix:
0 1
0 0.1 0.9
1 0.8 0.2
For any input (say, 0, in the top row), the output will be interpreted as either a 0 or 1, so the row sum must be 1.However, there's nothing forcing the probability of 0 as an output in one row to depend on its probability in another row. One could implement the gate above in software, with no problems, and a hardware equivalent could certainly be produced.
[Edit-- fixed row probabilities in second row.]