Because many people choose to purchase additional lenses. Many of the lenses still produced by Nikon, and those for sale on the used market that remain popular, do not have a focus motor in them.
There are also many third party lenses without motors in them.
So the reason the package a lens with a motor in it is it's a newer lens design with the motor in it that has other advantages (such as quieter focusing, speed, accuracy, manual override).
So I guess it's not so much they put a lens with a motor in it with a camera that doesn't need that lens, it's more they put a motor in the camera so the user has more otpions beyond what came in the kit.