When I use Ninja Boy to swap out a heavily damaged EX Pokemon for one that is not an EX, if there's enough damage to KO it does the opponent take one prize or two?
Since the swapped in Pokemon is not an EX Pokemon, your opponent takes only one prize card for the KO.
Source: Steam Siege FAQ (2016-08-04), TPCi Rules Team (2016-08-04)

Relevant cards

Note: All applicable cards may not be listed below.
XY11_103