Somthing similar happened to me when I ordered Deluxe Paint V from Software Hut a few months back. Got a CD-R in a thin jewel case. I recieved no manual either. Pretty lame. I doubt they have permission from the publisher (Electronic Arts) to distribute these obvious copies of their products.
On the other hand, I ordered StormC 4 directly from H&P last month and it came in a thin jewel case and only a semi-professional registration card for the insert. The CD was a blue CD-R with a nice, professional label.
My guess is it's a simple way to cut costs, but if the OS 3.9 CD doesn't actually have the boing ball logo on it I'd at least check with Amiga Inc. to ensure that the company you ordered it from has permission to distribute such copies.