Displacement is virtually identical between the stem with and without hole, which seems to indicate it doesn't make too much of a difference
It doesn't make much difference to overall stiffness, but drilling holes in things usually creates stress concentrations at which fatigue cracks initiate. Plenty of people have done it before, and not many of them seem to have died from it. I have a 12cm Cinelli 2A with a tapped hole in the top to mount a computer, and it's showing no signs of ill effects some 25 years on, although that's in very light road use. The people who usually drilled their stems were cyclo-crossers, who obviously gave them a much harder time than I ever did, and they are still doing it:
That doesn't make it right. The correct attachment location for the cable stop if you still insist on using cantilever brakes (and seriously? It's nearly 2015, get over it) is the fork crown.