This joint is a royal pain to cut on a dado set on a table saw if you are making a lot of boxes, since you have to make several cuts that require a different setup for each one. Commerical boxes are cut on gang saws (all the fingers are cut by separate blades on a mandrel at the same time, one pass per board, both sides), but I have to cut them one dado at a time. It's quite enough hassle to cut that many dados already, I don't want to have to do two complete setups. This is complicated by the current use of 5/8" deep rabbets rather than 7/8" rabbets, which DOES increase the strength of the remainder -- it's shorter and stiffer, hence less likely to get broken off, but unless you want to cut MORE dadoes, the top finger isn't the full depth of the rabbet any more.
This is the standard joint from Brushy Mountain and the old Kelley boxes, but I don't see any real advantage. Looks nice, certainly seals well, but I don't think it's all that much stronger. Kelley now uses the same joint I do -- the rabbet is the dado on the end pieces, all the dados on the sides are the same. Easier to manage during production, I suspect.
The strength in a box joint is not in the nails or glue, it's in the fact that you have substantial interlock between the boards. The main place that boxes get damaged, other than joint failures due to water intrusion and rot, is when someone sticks a hive tool in between the boxes and pries up on the frame rest rabbet. Doesn't take may events like this to damage it, it's not very strong, and it doesn't matter which way it's nailed up, prying on it will dent it.
If it wasn't such a pain, I'd use the joint you describe just because it looks better and is more likely to seal, but I don't think there is enough gain in strength to bother. The bees take care of any water leaks and will more or less completely fill any crack between the boards with a pretty decent glue.
Note that if you drive a nail at a 45 degree angle, you won't be putting it in the narrow part, it will be in the wide part. I wouldn't drive ANY nail into a 3/8" x 5/8" part, it will split if the nail is big enough to do anything besides look pretty.
Peter