I don't use queen excluders to keep eggs out of supers, and I've never had any issues with queens laying in supers. I usually over-super, but I'm foundationless, which means unless I have drawn comb laying around, I have to pull up drawn frames into the new super so they'll drawn straight, so I end up with the top two boxes half drawn when I add a new box. The only time I under-super is if a super is full of honey but not capped and I'm just waiting for them to finish drying it so I can harvest. Then that box is on the top and it's easy to just add an escape board and take that when it's ready.