>I know a queen won't walk across honey
Sure she will. She will walk across every inch of the hive, but she usually doesn't want to lay in what she percieves as a seperate area from the brood nest. A crown of honey establishes the top of the brood nest.
> but when I'm putting on a new super, there's no honey in there. I hate using excluders, but what can I do?
Since I use all the same size boxes and no chemicals, I'm happy for her to lay anywhere she wants. Using an excluder, IMO, often leads to swarming because the brood nest gets clogged with honey and the queen can't expand the nest. I also let them build drone comb and purposely leave it on the outside edges of the brood nest so the queen has somewhere to lay drone when she feels the need. Sometimes she moves up becaue there was somewhere she could lay some drone up in the super. Then, since there is already brood there, she lays some workers.
There are two instincts at work here. The queen's instinct (and the workers' instinct) to raise 10% drones, and the queen's instinct (and the worker's instinct) to keep the brood nest consolidated. The instinct to raise drones will overide the instinct to consolidate the brood nest.
If you'd like to prove both of these concepts try, during drone rearing season, putting a box with some drone foundation all the way on top of a hive that has two or more supers of capped honey, no excluder, and virtually no drone comb in the brood nest. The queen will find this drone comb in the top box over two boxes of honey (which she is purported not ever to cross) and lay it full of drone every time. If there is plenty of drone comb in the brood nest (about 10 percent of the comb is drone) then the same experiment will fail because she HAS enough drone comb to lay in to her satisfaction and her insincts are to try to keep the brood nest consolidated.
If it matters to you that the queen lays in the supers, you should use an excluder. It does not matter to me. You can do several things that are a little easier on the bees. You can use an unbound excluder as a "queen discourager". Just rotate it 90 degrees so the long ends stick out and there is a gap at each end of the excluder. The bees can easily get to the next box (as can the queen) but the queen, because of the barrier of the excluder in the middle, percieves the area above the excluder as a different area and doesn't want to lay there. Also you can leave an upper entrance so the bees don't have to squeeze through the excluder to get to the supers.