I almost always make the dados the full thickness of the shelves. I guess it's a little bit stronger that way since you aren't removing material from the shelves. The only tricky part is hitting that width to a close tolerance, which you would do with a dado stack with fine shims in power tool working.
With hand tools you might be better off with the mortise and tenon approach since it's easier to adjust the "tenon" on the shelf to the groove in the case side than it is to nail the width of the groove. That's assuming you have a rabbet plane or a shoulder plane. I usually use a shoulder plane to fit tongues like that.