I have a mixed answer for you. I apologize in advance for the length of it but I really want to give a detailed answer.
I believe that pet store rabbits that are taken from their mother too young - have a higher incidence of health problems - largely from being taken from their mom too young. I think the stress of separation can cause health issues. Can I prove it? No.
I personally believe (and understand - this is OPINION only) - that a rabbit from a RESPONSIBLE breeder has a greater chance of not having health issues. I also believe that it may potentially be better socialized to begin with.
Why do I believe this?
First of all, the baby spends more time with its mom. It has less stress (hopefully) at weaning because it isn't taken away at 3-4 weeks of age. It also spends more time with its litter mates and I think that helps with the socialization and health issues. One of the things I love most about my litters is watching the kits interact with each other and with their mom. I think that they need that time with each other.
Secondly, I believe that baby is better socialized from dealing with the breeder on a regular basis. Once my kits have their eyes open, I try to handle them on a daily basis to check tehm for any health issues. They are used to being handled. Depending upon their temperament, by the time they are 3-4 weeks old, they look at my coming to open the cage door as a fun thing and they come running to see me. They know me and trust me. I frequently will bring them a cheerio or something and they see people as "fun".
Thirdly, as a breeder, I can tell you about my kits and their health. I watch regularly for health issues and can start treatment THAT DAY. The kit will not sit alone in the back corner of a cage for more than a few hours before I'm there attending it.
Finally, as a breeder, I do my breeding with certain goals in mind.They might be for body type or for mane (I breed lion heads) or for certain colors and patterns. For example, when it comes to breeding broken lion heads, I'm particular about them - but I am breeding largely for pattern and temperament (vs. my "show litters" where I'm breeding for other reasons). I'm not going to simply put two rabbits together to mate and say "there you go".
With all that said, I have known breeders who have placed some of their babies in pet stores. Most of them wait until the kit is 6-8 weeks old and the kits are gone within a couple of days. Many times they've made arrangements ahead of time and the store has said they'll lionhearted on X day. The pathetic thing is the breeder might get $5 or maybe a whole $10 for the rabbit....whereby if they sold it themselves they could get a lot more...but many times they only want to be known for selling show bunnies....so they sell take their pet quality rabbits to the store.
I think that if you really want to buy from a pet store, make sure they can give you the name of the breeder they got the rabbit from and the phone number. Contact the breeder and talk to them. Really look at the rabbit - does it look like it was too young to leave its mama? I know you want that cute, adorable little bunny - but I'd hate to pay $50 or so for a baby rabbit and then have it die a week or so later.Know what I mean?
Once again, this is mainly opinion based upon what I've seen and heard.I think that the issue with pet store bunnies is mainly "Were they taken away from mom too young?" If so...I think you're going to potentially have some health and maybe socialization issues..
Just my .02
Peg