If you sub for the qb, they will play more people in the box on defense. If the qb is still in the game, split out or whatever, he could still do a shift and get back under center and throw the ball. So as a d coordinator, you would be hesitant to pull your safeties down until the last minute. Also, as you mentioned, the double pass is still in play. Plus, even though the qb may not be a good reciever or blocker, he still has to be accounted for by a db, so you still should get the numbers you are looking for when running the ball between the tackles with your wildcat back (hat on a hat).
With all of that said, I can see your point, Sundance.