It harms very much because bees must heat the vain room.
Heat rises up and bees are like without cavity shelter.
If you think youself in a smal room. You generate heat and the room is warm. But if you are in 100 persons room, your heat means nothing. It just escapes.
It means too that room is cool and the breathing water condensates inside the room.
So, keep wintering room tight, and if the food is near to finish, ad the super and bees have again a proper space where they have warm interior in top most box.
.yes, wintering hive is not right place to store extra boxes, are they full or empty.