Hive combining successful... but wait, there's more!

I went into the new hive today to see how the combining had turned out.  In the few days, I had seen only one more small piece of newspaper on the ground and no dead queen bee.  I inspected today without smoking the bees.

Medium super with 2 frames removed

Chewed newspaper in place

First I noticed that there were still a lot of bees in the medium super, the one into which I had put the frames from the nuc.  I just took the box off and set it on the inverted cover without inspecting it.  The bees had done a pretty good job on the newspaper.  There was a large part gone from the center and a smaller holes at the edges.  I knew the old and new bees were able to get together and the new bees had a way out of the hive.
The next box is the top deep box.  It was pretty much empty with frames without comb and only a few bees hanging around.
Then, the bottom box.  Lots of bees, as before.  I had intended to take out the drone frame and replace it with a regular frame, but it had some capped honey and nectar in it.  No capped brood or larvae, so I left it.  This was just about the only honey in the hive.  On the remaining frames was capped brood and larvae of various ages.  Then I spotted the queen, fat and golden.  All's well, I figured.
I put the boxes back on and inspected the medium super- very little honey, capped brood and larvae, and another queen!  I have a two-queen hive!  I put everything back together and went to look up what to do.
The two queens are separated by the empty deep box.  I guess there are essentially two colonies in one hive.  Beekeepers do make two-queen hives because they produce more honey at a lower cost.  When this is done purposefully, they use a queen excluder to keep the queens apart.  I also read that 10% of colonies will naturally have two queens, often in the spring. 
I had wondered what I should do; nothing or remove one queen.  It is clear that I should do nothing.  The bees will figure it out themselves.  In the meantime, I expect the colony(ies) will quickly enlarge.  It needs to start making some honey stores.
I also hefted the top super on the old hive to check its weight (an indication of honey storage).  It felt like only a few pounds.  I'll check again in a week to see if it feels any heavier.