The worst thing that is going to happen if your cones are bad is that your bearings will wear faster. You can replace all the bearings in your hub for around $1.00~$2.00.

It will cost you more than that to replace the cones IF you can get the correct cones.

Unless you are an extreme high performance rider who might notice the minimally greater resistance due to the imperfect cones, I say use the cones as is and change your bearings every 4,000 miles or so.

Your cones and cups should be of harder material than the bearings so there is little concern that the cone damage will be transferred to the cups.