Pro shops are only sustainable if they adhere to business models that ensure profitability. If a shop owner devalues his services by mostly punching holes in outside balls at bare bottom pricess, he won't be in business very long. Once a shop gets this reputation, in many cases it's the beginning of the end. I've seen it more than once.
I didn't say anything about bare bottom prices or say that's what they should "mostly" be doing. As someone else posted, if a shop bumps their normal drilling fee by $10 over their normal drilling charge for a ball purchased outside, that's fair. But to say "I won't drill a ball not purchased here" or to say the cost for drilling two holes is $100 (which is essentially saying "I won't drill a ball not purchased here"), THAT'S the beginning of the end.
If the OP brings in a used ball and asks for a plug and drill, should he then also be charged an extra fee because the ball was not originally purchased in that shop? If he wants it resurfaced, should he be charged more if it wasn't bought in that shop?
If I buy a new, non-discontinued ball, I buy it at my proshop and have them drill it. If I see a great price on a discontinued ball, then I do that and have my proshop drill it. I don't see an issue with that, and neither do they. And they do quite well.
(To be clear, I'm also not a jerk about it. If they want to take a couple or three days to do it...or even a week, I'm perfectly okay with it. I'll take the slow road since they are doing that for me without complaint. Perhaps attitude is a driving force in the original scenario.)