Maybe this is a stupid question, but could you easily spot larva and eggs before??? If you have capped cells, the queen was there 15 days ago (give or take a few day)
Do you see any new QUEEN CELLS being constructed anywhere???
No matter what, get a strong sun behind your shoulders, use a good set of reading glasses 1.5 to 2.0 from the dollar store and you'll see either or both if they are there.
The queen taking a break is not common UNLESS there is simply NO ROOM to lay eggs, but I've seen her lay on undrawn cells and then workers building comb around the eggs.
Lastly, are your bees still as active as they should be - I doubt something happened that caused a queenless hive, capped cells, but lack of pheromone all at the same time.