Theoretically, yes, you shorten the weight block. You will inevitably change the weight block no matter how you drill it, however, and it doesn't have any more effect than drilling the ball anywhere else simply because it is through the pin.
As far as how drilling effects RG/DIFF, studies are still under way to try to firm up those answers. Often times, you can get different answers as to the effects of drilling a fit/extra holes from different tech departments. Realistically, all of these tech departments employed by ball manufacturers are filled with knowledgable people. Do we really think any of them don't know what they're doing? No, it's just one of those situations where many people have reasons/research to back their opinions, but the answers aren't definitive enough to become a true science yet.
I'd imagine the real answer to your question would be- It depends- What was the core shape originally? How big is the core exactly? How deep was the hole that was drilled? Inserts or no inserts? ETC.
It's almost unrealistic to expect any pro shop professional to have 100% of these answers. The key is, go to someone you trust and can back their opinions with logical thoughts. Also go to someone who is knowledgable with manufacturer regulations and suggestions. If you are the driller, hopefully you fit under that category. If you do not, strive to get there. We all start somewhere. I know I didn't pop out of the womb with any great knowledge of physics.
Anyhoo, kind of rambling now. I don't personally think there's anything wrong with drilling out a pin. I have a couple balls drilled that way that roll fine.
