You're right, the front brake housing should be threaded through the hole in the stem, that's why it's there. But it also looks like you have a separate cable hanger atop the headset. That cable stop makes it a lot easier to set up and adjust the front brake than without it.

I think manufacturers thought back then - which was cheaper, drilled stem or cable hanger, and the drilled stem won in many instances, though some have both. It's not ideal IMO to have a drilled stem only. The danger is that if your threaded stem works loose during a ride - say riding on bumpy or rutted roads without being properly tightened first - you lose not only steering, but your front brake as well. A $3 cable hanger is a much better solution.