belay loops are used to belay to prevent tri-directional loading on carabiners (miscalled tri-axial in some books). they are ridiculously strong due to their construction of doubled webbing.
the reason for tying into the harness directly is simply a matter of wearing out the belay loop too fast. as i said, they are plenty strong. If you're breaking these parts of your harness in a fall, there are other issues to deal with, like imploding internal organs and such. Personally, I feel better tying in through all 3 spots, the waist belt, belay loop, and leg loops on my harness. That way, if I happen to miss one, I'm still connected to it via one of the others.