Runes in shop is bad but it's the chests that is really bad as there is no limit of any kind there. Some of the mega whales likely alreday have there entire temples maxed as $10k is a normal week for some of them.
Please re-read. This affects old and new towers exactly the same. Also it's not a bug, it is an intended change to the looting mechanic to address along standing issue with high level players with very low level walls.