"If pollen is being stored elsewhere, then there is a problem with that hive design."
I can assure you that there is no problem with the hive design. I use the standard 5 frame deep nuc boxes both for honey collection and for confining the queen in the bottom box with a QE on top.
Beekeepers have this belief that you cannot make honey and bees in the first season. In this little experiment, I have 2 deep nucs storing honey above. Follow by 2 brood nest in the middle and the last brood box is for the queen to stay in. The top deep nuc box full of honey/nectar is about 60 lbs. each. The honey are 90% cap now. And our main flow is not even on yet because of cooler weather earlier this season. Maybe in another 2 weeks that our main flow will be on mainly privet nectar.
Lots of young bees and pollen stored in the box above the brood nest. You cannot see a single cell of either nectar or pollen in the bottom brood box. So it is not the hive design but rather the hive configuration that I put the queen into. These are the standard deep nuc boxes that ML sells. I got them last year on the holiday sale.
If you don't believe me then just before the main flow set up a 5 deep nuc hive to see for yourself. This hive is run by this season's early Spring queen that I rear.
First year, 5 deep nuc boxes collecting honey:
http://imgbox.com/3qO9iqWg