Bees don't like honey below them - they prefer it to be above and behind - so they can protect it. During winter they will munch their way upwards, so a winter visual check can reveal the level of stores by how high bees are in the frames. If they are flat against the crown-board, you might have a problem. If they are way down, there's plenty. You can always take a photo from underneath as well to see that they are alive and kicking in winter.
Putting frames under the brood box is a good way of getting them emptied. I use the technique also when I have some granulated OSR honey in May. In this case, I close off the entrance and put an eke (spacer) with an entrance between the super and brood box. It can take a while for them to clear the (crunchy!) honey in this case.
I tend to nadire a full super of stores under a fairly full brood box at the end of September with no queen excluder. Come spring, the super is empty and bees have not gotten around to laying in the super that's underneath yet. And no, there's no need to bruise the cappings. Bees put the cappings there and they are quite capable of removing them when the need to.