You are correct. The atmosphere within a honey bee colony can increase in CO2 as the bees pack in their winter cluster. So while bees experience an atmosphere of around 0.10-4.25% in summer, it increases to 4-6% in winter, which is higher than the air outside the hive (~0.035%). Certainly, honey bees can sense CO2 through specialized receptors on their antenna and have been shown to regulate CO2 within their bodies by opening and closing their spiracles in a way that flushes out CO2 from their bodies. Also, at the hive level, when CO2 starts to reach dangerous levels (~10%) bees will use fanning to move CO2 out of the colony. Combined this makes honey bees one of the insects most adapted to living in high CO2 conditions. Notably, there is some evidence from the University of Manitoba that varroa mites are not so well-equipped and they experience elevated mortality above 2% CO2. 

But they key message here is to ensure your colonies have an upper entrance going into winter.  Not only does this entrance help bees void stale air, but more importantly it helps them void the real killer of hives over winter, moisture. I recommend that in addition to an auger hole in the top brood chamber (or upper entrance) make sure to place 1/4-1 inch rigid insulation under the lid to ensure any moisture coming off the bees doesn't condense and drip back down on the bees.