They may have just gone through a mass emergence leaving a lot of open cells. The queens will go back and lay them out, but yes she will lay much smaller patches this time as she works across the nest. The bees will be backfilling the nest with honey constraining her to those smaller brood patches. There will not be a brood break. Just patches about 1/4 to 1/3 the size that you had been seeing up to now. Check in a week, you will see what I am describing.
The other possibility is those few hives you noticed that have little to no brood with polished cells could be on the tail end of a supercedure that is in progress. Meaning there is a virgin or newly mated queen in there that they are expectant will startup in those polished cells very soon. Make some notes in your apiary notebook and keep an eye on those hives as the failure rate of late supercedures is high. Same prescription, check in a week to see that there are small patches of eggs/brood laid to confirm their SC success. If you have nothing in a week, then you have a problem and some hard decisions to make.
As for queens stopping laying and going broodless. The extent that they slowdown/shutdown really depends on the strain of bee as well as your area and climate. I am in the far North and run a carniolan/caucasion mix. Personally by investigative experience, ie inspections mid winter, the hives are never truly broodless. They always have a small patch on the go in the centre of the cluster. In other words, queens never shut down completely. If you have a queenrite colony, you should always be able to find some brood in there at any time of the year. Mid winter it is going to be small, maybe only 50-150 cells, but it will be there.
Oh, and the other tale/myth. The bees will kick out all the drones in the fall. Yes, but no. They do not toss every drone. They definitely carry some through the winter, 20-100.
Hope that helps!