Buying directly from a reputable breeder is best, but I don't consider buying from a good pet store to really be worse than buying from a dealer at an expo. (The expo dealer is going to be tons cheaper). Pet store animals are retail/pet priced. Animals purchased from breeders will be priced with consideration of shipping costs in most cases. (For example, a normal ball python in a pet store sells for 60 to 75 dollars. A normal ball python from a breeder costs around 25 dollars, but then you will have to pay 35 to 50 dollars in shipping charges).

Find a local breeder, and you can get the best deals of all.

The store you mentioned doesn't sound awful--all of the animals came from a single known source. Ask the store if they offer any guarantees on them, and ask what their procedures are for preparing a cage for new arrivals once all the animals in it have been sold out. If they all look healthy, then they're as safe as most, and safer than some. I don't demonize pet stores simply because they are pet stores--nor do I expect them to house animals in optimal permanent care conditions--as long as the animals are good body weight and aren't around for very long, cage sharing with animals of the same species is normal for pet stores (and also very frequently seen at expos).

If that's your only source for those animals, and there is one there that you really and truly want, and are willing to pay a pet store premium for, then go for it--just remember to quarantine. A year is the new 'safe' quarantine period, though, not the 3 months normally cited. But quarantine is necessary whether you buy the animals in person from a top breeder, or anonymously from a pet store.

My friend's pet ball python came from a local pet store--a knowledgeable place that even revealed that the original breeder was crestedgecko.com. He's completely healthy, hardy, and growing just as he should. Not all pet stores are bad, and while they aren't generally the top choice for purchasing animals, I wouldn't write them off completely. As long as you know a good store from a bad one, and know which questions to ask, I see no reason to dismiss retail stores out of hand.

In fact, NERD has a retail storefront.