I'm not sure I would of given a new package of bees 2 deeps to start with. A single deep would of been plenty of room for them to start and then when they get 80% of the first deep drawn out then add the second deep. Bees naturally build queen cells all of the time, for that just in case emergency. Most of the time they will sit empty until they decide that something is wrong with the queen or are tired of her and are going to supercede her. On your inspection did you see eggs or larva. Its probably too early for capped brood but look for eggs or larva, if you have those than the queen is present and laying.