They have switched to digital manuels instead of the original physical paper ones. If you open a game app, it will take you to the home screen of that game app where at the top is a picture of a manuel that you can tap on to open the manuel.
Only game I know of that has a paper back manual is Disgea 3. Other then that you really never get anything beyond a piece of paper or three pages.
@OP - Really the cases look like Sony wanted to save money and not make new molds. Instead just make a small plastic injection mold instead of a whole new mold for a case. Which in the end makes sense.
This is a smart idea since it'll use even less plastic than before, plus, no paper manuals means they can save trees. ^^d
I don't like that i like buying games with physical manuals. Oh well i guess.