Decoupling capacitors on opposite side of board when using PCB mount EMI shield
It seems to me that you are kind of asking how you should make the topping of a cake so that the cake will be excellent. 

You might not need an EMI shield at all if you take care on component placement and layout. In general, proper signal routing has much greater influence on EMI reduction than shielding. So the shield is the last thing you should care about.

So my answer is: Place the caps where they are best for the circuit, then care about the shield.