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Pathfinder Rulebook Subscriber

Only one stat will apply. From the Ninja's Ki Pool text (emphasis mine):
PRD wrote:
If the ninja possesses levels in another class that grants points to a ki pool, ninja levels stack with the levels of that class to determine the total number of ki points in the combined pool, but only one ability score modifier is added to the total. The choice of which score to use is made when the second class ability is gained, and once made, the choice is set. The ninja can now use ki points from this pool to power the abilities of every class she possesses that grants a ki pool.