I vote you make the notches longer and get rid of the cleat. It looks cool but will get in the way.
Are you going to nail or screw your boxes together?
I like gorilla glue and screws myself.
They are already glued and screwed. Well, just glued in those pics, now screwed, too. All the screws are hidden though. On the cleat I went from the inside to the outside without going through all the way, and on the box joints I went down from the top (I know, you wouldn't think it would work, but it absolutely prevents them from moving).
I went all the way to the top with the cleats because there's a lot of glue and not so much screw, so if they're going to hold 100 lbs, they need a large surface area for the glue. There's a few ways I could deal with that when it comes to the top. The first would be to cut notches in the cover, the second would be to have an extra-long top, and the third would be to put in an extra-tall inner-cover. Or, I could try to make the cleats shorter at the risk of having them pop off when I go to lift it when it's full of honey.
As far as the length of the notches go, they are plenty long enough to fit my whole hand.
EDIT: another option I just thought about would be to simply top it off with one with a shorter cleat. That would disallow me from swapping around that super, but I could always swap the individual frames if need be.