Layne Westover raised some good points:
1. In our climate, by which I mean most of the US, I can't imagine running
supers over a two-queen hive configured as mentioned by Tom.  The beekeeper
would need a ladder to get through the flow!  While I know of three
beekeepers using such a system, all reduce to one colony for the flow.  For
that reason, only one queen excluder would ever be necessary.
2. The three beekeepers I know only use the excluder while there are two
queens present.  As soon as the top hive is taken away they remove the
excluder, figuring the top hive body on the bottom hive is so packed with
honey a queen will not cross it to get into the comb honey supers.
3. While Layne is surely right about a supercedure queen not being able to
get back into the hive through the drone escapes, this system is only used
in the spring/early summer, when beekeepers do not worry much about
supercedure.

A "better" two-queen system that is used involves setting up two nucs in the
spring in one hive body.  Of course, the nucs are separated by a divider
board.  Above the deep is a medium, also separated by a divider board, and
above that is a queen excluder and "lots" of supers.  With new queens and
all young bees, the swarming impulse is minimized.  Two queens produce a lot
of brood, making a huge field force available for summer (July and August)
flows.  The advantage of this method is that the stack never gets as high,
and the beekeeper avoids the work of moving the top hive.  The disadvantage
is that the carpentry has to be reasonably precise so that the divider
boards for the deep and the medium match up.

Lloyd
Lloyd Spear, Owner, Ross Rounds, Inc.  The finest in comb honey production.
www.rossrounds.com