Queen excluders are a hinderance to the bees and they don't like them. They have to persuaded to go thru them. Let's face it, if you had to tightly squeeze thru a tiny door to get into a room of your house, you would think twice and really make sure it was worth your while before doing it. Queen excluders work when used right, but there are other ways to accomplish the same thing without them.
Bees will not go thru an excluder to draw foundation in an added super. They will just honey bound the hive below the excluder, reduce nectar collection, and even crowd themselves enough to swarm before drawing foundation above the excluder.
Yes, without an excluder the queen will lay brood in your honey supers. So what, brood is a good thing. She will eventually be pushed back down as the bees fill the recently hatched cells with honey before she can lay in them again. Passing up on the few frames that may have some brood left when you go to extract is more than made up for by the "extra" honey from not using a queen excluder. Unless your trying to make comb honey, brood in the supers is not a big deal. With the new cartridge type comb honey systems, excluders aren't needed anyway.
If you insist on using an excluder, put it on 90 degrees off, so there is a passage in the front and back for the bees to pass. The queen spends most of her time in the center, and most likely will not bypass the excluder. Then again excluders are not 100%, queens have been known to force their way thru.
The only real use that I have for an excluder is when hiving swarms. If you put a queen excluder between the bottom board and the brood box until the queen starts laying, there is less of a chance they will abscond.
Queen excluders are a "good idea" in principle, but most of the time the negatives outweigh the positives.