It will affect the handling, the amount depends on how much you lower it. Whether or not it "hurts" the handling is up to you to decide. Lowering the rear in relation to the front, in effect, slows down the steering. High-speed handling is a little easier, slow-speed handling is a little more sluggish, but like I said, the amount depends on the difference. I have rear shocks that are about 1 and 1/2" inches shorter than stock, and pushed the front forks up in the triple trees the same amount to off-set the difference.