No, it doesn't adversely affect the performance of the ball.  I've even heard from some pro shop operators that drilling through the pin will make the bridge less susceptible to cracking, as compared to drillings with the pin near one of the finger holes.
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Better to be a big fish in a small pond than not to be a big fish at all.

Horrid in Doubles, torrid in Singles...
...that's The Curse of Dusty.