I don't think he's so much killed them. I think it's more like failure isn't an option for them and they don't like leaving potential captives who can potentially betray them, which is why they dissolve into green mist upon defeat. It's more or less The Hand's equivilent of a cyanide capsule. In the original Miller books, if I'm remembering correctly, while Matt has always beat them, he never outright killed any.
And while it's been awhile since I've read the issues, I think Millar (Mark, that is) alluded to the fact that many Hand ninjas aren't so much alive as they are animated corpses who literally gave their lives to even join The Hand.