I live in a small, semi-rural community, with a locally owned and operated pet store. I have been dealing with the owner for years -- sometimes as a customer, but usually as someone who stops by and gripes about things I see in the store. I can only speak for the way in which this particular pet store is run - it's different with every store, and especially within large chains - but here is my input/observations, for whatever it's worth:
1. The local pet store buys most of its guinea pigs from a breeder. From what I can tell, he essentially "orders" pigs whenever the breeder tells him a new litter is ready, and either they deliver them or he picks them up. It's a two-hour drive to the city where this breeder resides. Nothing (as far as I've been able to determine) is really known about the genetics of the pigs being bred.
2. No effort is made on the part of the pet store owner to determine sex or breed of the pigs; sows and boars are housed together. I've repeatedly found males and females together, and have repeatedly shown the owner how to determine which is which.
3. The living conditions are poor. Guinea pigs are housed in small, dirty aquariums. They are fed a very poor quality diet, usually no hay, and I've seen several cases of urine scald, fleas and signs of mites. Nails are not trimmed, baths not given.
4. There is no effort to diagose or treat illness. To my knowledge, new pigs are not quarantined. When I found a pig who had a very obvious headtilt, the owner was surprised and said he'd talk to a vet. The pig disappeared, never to be seen again. I cringe to think what happened to it. Another time, I found an adult boar with an anal impaction nearly the size of a golf ball. I spent nearly an hour removing it and showing an employee what to look for. That employee is no longer there.
5. Pigs that aren't purchased from breeders, have been dumped there by people in the area who can't be bothered with them any more. No attempt is made by the pet store to determine the history of the pig, the sex, health, etc. No effort is made by the pet store to ask that the pig be taken to the Humane Society, where it might be fostered and given a good home.
6. When a guinea pig is purchased, no effort is made to provide ACCURATE information about care. I gave the store a hand-out sheet at one time, but I doubt seriously that they still provide it. They push the products that they sell, which is crap: L&M brand pellets, crappy hay (usually alfalfa rather than timothy), a tiny cage, inappropriate bedding, a mineral wheel (an emploeye was absolutely floored when I told him that not only are these unnecessary, but may also be harmful), etc. Most employees not only know nothing about the animals they sell, but they couldn't care less. It's just an after-school job for most of them.
7. No effort is made at any point to educate customers about the dangers of breeding; it's not unusual for a pig to become pregnant (since pet store employees have no idea how to sex pigs), and the customer brings the offspring back to the pet store to be sold. Thus, the cycle of potentially bad genetics just goes on and on.
For these reasons, I feel it's better to support rescue than pertpetuate an industry built on bad practices.