So weapon finesse says, "If you carry a shield, its armor check penalty applies to your attack rolls."
My question is, if you're non-proficient with a shield that you also take it's ACP as a penalty to attack rolls. Does this double up and stack or does it only apply once?
Once. It's the same penalty from the same source [shield]. It's just different triggers for the same effect, [using weapon finesse] and [non-proficient].