I wouldn't drill the trusses. If you worried about support/protection, you could nail a piece of 1x3 strapping to the truss then staple the Romex to that.
Question on wiring behind knee walls. Can you staple to the backside of the 2x4 rather than drill through? I will be insulating under the roof decking so no insulation interference. This will not be an easily accessible area.
Like in the pic.