I have been wondering this for a long time, and thought I would see what people think about it.

Do you see the pin in such an important role, than if it cracks it is going to hurt the ball? I don't, I only see it as an indicator for layout purposes.

Let me give you an example, people make a big deal if the pin is drilled through. I don't. Another example, a friend of mine has an Apex Adrenaline that cracked around the fingers, and the bridge started to fall out. He plugged it and the pin was gone. As long as he knows where the pin was, or atleast is close to where the pin was, do you see this as a big deal?

I see it as nothing more than a drilling tool to use so you can see where the core is (basically).

Am I viewing this wrong? Is the pin actually being there so important that if there is a crack through it or if you drill thought part of it that it actually HURTS the ball?

While I agree with everyone that a cracked pin won't affected ball reaction, it can hurt the ball.  Once part of the cover starts cracking, more cracking can occur if you don't take care of it.  As was mentioned, plugging the ball is usually sufficient to fix the issue.

You can recreate the pin with plug.  I had a ball that put the pin at my ring finger.  I didn't get the exact reaction I expected, so I plugged the ball and gave it to by brother-in-law.  Since the pin was gone, I greased a pencil and poured the plug around it.  After the plug setup a bit, I removed the pencil and plugged the small hole in a different color.  Now the ball has the pin back.
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Good luck & good bowling