I cushion more delicate items with softer ones and use zip-lock type bags for moisture protection. Then my compression straps on the panniers hold everything in place to prevent any damage from jolts. If your bags lack compression straps just add them around the rack and bags.
If your pannier mounting system is weak or loose damage to the bags may occur just as using low rider racks on gravel or worse surfaces brings your bags nearer to potential projectiles which will damage the bags.
My full fenders also keep rocks thrown up by the tires from hitting my bags.