True, some rack systems are tenuous at best, but others are bombproof. You really have to evaluate each individual installation when making the decision to use bow or stern lines or not. I certainly wouldn't trust most factory rack systems, since most are mainly designed for securing luggage.

To pull the rack (a Thule) off my car would require major bending of the door and window frames, which are some of the strongest sections of the roof. With the boats seated inverted in the saddles, at 70 mph on windy days, they don't even move. Consequently, I don't feel the need for bow or stern lines, though I occasionally use two straps on the front saddles. I certainly wouldn't discourage anyone from using bow and stern lines, but they're not an absolute necessity if your rack system is stong enough.