If you live somewhere where you have the option of rescue, I would look into that. There are a lot of guinea pigs that need homes. That said, there are some countries and locations where rescues are abundant and some where the option is not available or really difficult, so I sympathize there (and honestly, mine are from the pet store because there is only one rescue in my area that only adopts out bonded pairs and because of the age gap of my pigs, I am always wanting a solo pig to bond with a pig at home. We started out with a same-age pair, but unfortunately one dramatically outlived the other and since then we have never had the option to take on a pair at one time.)
The purpose of show breeding is to produce animals with proper show conformation and not necessarily to produce good pets who are friendly, accustomed to being handled, etc. With fifty pigs, it is likely that there is not much time to socialize the babies (or the parents) before you bring them home. With some species of dogs, etc., when you buy from a breeder you are at least getting genetic testing common to the breed, for things like hip dysplasia, etc., but to the best of my knowledge there is no genetic testing for issues available for guinea pigs. Realistically, this breeder is either mass-breeding for profit or breeding for show conformation (which leads to lots of left-over pigs who aren't show-quality who are then sold as pets.) Which doesn't mean they won't be nice piggies... just that I doubt this breeder is spending much time with the pigs before they are sold, or with their parents, for that matter. That said, I honestly think that most pigs out there are the product of breeding for profit or accidental breeding or backyard breeders with no real clue what they are doing, whether you are getting them from a pet store, from a breeder, or from a rescue (because prior to coming to the rescue, those pigs likely came from one of the above sources first.) So, in short, if possible, I would try to rescue. If it's not possible (and I totally get that in some circumstances the option is just not available!) you will be looking at breeders or pet shops and I'm not sure there's a huge difference between the two options in terms of the care of the animals involved.