Of course, while I was busy panicking, a fourth - somewhat more probable option - totally escaped me: (4) Incompetence.
Waaaaay more likely is that during the previous inspection, I had managed to transfer the queen into the supers. The result would be that she would lay new brood above the queen excluder (which is what I found) and there would still be brood below the queen as per usual... Grrrrr.
(What's more, they may have swarmed during the week as well, although when I looked in the hive there were still *masses* of bees.)
Visit http://website.lineone.net/~dave.cushman/excludertypes.html for an excellent description of queen excluders