Pahoo- I have seen spent caps in the hammer cup but it was due to using the improper size cap.
Quality caps with the properly sized nipple will not (IMHO) have a problem with caps stacked in the hammer.
Again, in my opinion a nipple (both hot shot and normal) have a life span. When they are new and if well made they work well. As time goes by they start to erode due to the force of the cap spark and vent back from ignition. When a nipple starts to wear it allows more and more vent gas to escape through the nipple hole.
In time this causes all sorts of problems. I have seen cases where the problem was so bad that the hammer would go to half cock after each shot. This amount of erosion would cause a significant safety issue with any type of nipple.