While it is not harmful to the golf cart to be jacked up and will not cause any damage to the vehicle, it is not recommended to jack your golf cart up and leave it that way for long periods. It is good to jack up the golf cart only when it is time to replace the tire or work on the vehicle.  And, if you follow the proper procedure properly, install the jack in the proper place, lift and lower the cart very slowly and carefully, you will not have problems.