Two reasons:
a) Make a ball legal. Check on a do-do scale if the ball has too much (positive) side weight, AFAIK 1 ounce is allowed. A weight hole (most commonly placed on the PAP) just reduces this side weight, and can affect ball reaction, depending on where it is placed and how deep/narrow it is.
b) Tweak ball reaction. Sometimes after drilling you might want to slightly alter the ball reaction. Besides drilling thumb or finger deeper, a strategically placed extra hole can offer some additional options, e.g. reducing or increasing flare, stabilizing the ball's roll, etc., but these are just minute changes.
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DizzyFugu - Reporting from Germany
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