No issue, assuming you are talking about the tar strip plugs? They'll just pull it out, ream it out, and throw in a patch-plug from the inside. If they do it right and clean/grind the rubber ridges down on the inside before vulcanizing it in, they'll last the tire. Just never use fix-a-flat or they'll hate you. And most good places will only do a repair in the tread of the tire.
I was pretty good at them when I did that stuff. $50 sounds a bit high, but it does take some time to do right. You're still lifting up the car, removing the wheel and tire, waiting on cement to get tacky before throwing it in, rebalancing it after. It's not a 5 minute thing.