No, you are right. AP does not work against shields. However, I doubt there is a special armour calculation for projectiles based on their arc. More likely this is caused by the AP effect, or perhaps because slingstones traverse more of the formation than do arcing weapons.
In vanilla R:TW hoplites also used phalanx formation, so this was not a concern to the programmer. But I agree that the pike formation would not have provided much protection in reality.
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