Would Giratina EX's "Shred" attack allow my opponent to knock out my Shednija (with "Empty Shell") and take a prize since the attack says its not affected by any effects on the Defending Pokemon?
The damage done by Shred is not affected by Empty Shell, but that has nothing to do with whether you take a prize or not. You still get no prize because of "Empty Shell".
Source: PUI Rules Team (2006-01-12), Dragons Exalted FAQ (2012-08-23) Dragons Exalted FAQ (2012-08-23)

Relevant cards

Note: All applicable cards may not be listed below.
EX8_14
BW6_92
BW6_124