I would drill the top tube in a similar place to where they usually are. Probably close to where the existing rear brake cable stops are. Then with a pin punch or even just the parallel shank of the drill lever the holes a bit so the housing can enter at the appropriate angle more easily. Then run a continuous brake housing from lever to frame. An advantage of this is that your sweat won't get into the brake cable and corrode it.
If you were worried about structural integrity you could fix the housing to the outside of the top tube by other means and not drill it.