I'd be worried about the future babies. If the pet store wants to breed, they should probably get their own breeding pair. If they don't care enough to get a pair with known (and good) genetics, they probably don't care enough to make sure the babies are cared for properly.
Personally, I would never stud out my male to a pet store because of ethical issues. The pet store probably is in it for the money and just doesn't want to pay a breeder for baby dragons that are healthy, well-started and of good genetic lines. They may sell the babies before they're old enough, and they might not feed them or care for them properly.