Yes, a side-fan can still help, even with a totally enclosed cooler. Heat still radiates from the back of a GPU?s PCB irrespective of its cooler, and a side fan can cool it. My 230 mm side fan on my old Armor used to lower GPU temperatures by about 2-5 C.
That said, I haven?t bothered mounting a side fan on my Antec 902 yet because even without it, the cooling system is far better than the Armor?s, and I still have far lower temperatures.
The best option is to experiment with your case and see whether a side fan benefits.