What are your goals for your chickens? Are you looking for show chickens, eggs, meat, yard art, bug management, or something else? Do you plan to breed them or sell hatching eggs or chicks? Basically, what quality of bird are you looking for? What do you consider quality?
Feed stores get their chicks from hatcheries so I'll lump them together. Hatcheries supply the mass market. They want to supply a chick for a reasonable price that generally meets the breed requirements. They each have their own personnel (often family) that manages the different aspects of their operation. That includes the person that decides which chickens get to breed.
Most hatcheries use the pen breeding method. That's where they have a number of males mixed with a number of females to get random breeding. They carefully manage the numbers to get practically 100% fertility. The person selecting which chickens go into these breeding pens have usually studied genetics and the Standard of Perfection (SOP) so they know what the breed should look like. Due to the random nature of matings they do not control which specific rooster breeds which specific hen but you wind up with chickens that look like the breed is supposed to. The SOP is what the breed is supposed to be, each country has its own requirements. Some breeds can look a lot different from what the same breed name looks like in another country.
People breeding for show know the SOP and carefully select which male is mated to which female to give them the greatest chance of getting a grand champion. Even with this careful selection of breeding pairs or trios the majority of chicks produced do not meet showbird requirements. This specialty breeding is much more expensive than the hatchery method so the prices for these birds are usually very high. Show chickens often get rewarded for being fairly large as compared to hatchery birds. That's a common complaint against hatchery birds but they are not bred for that size and are not fed the diet to achieve that size.
Then you have others breeding for different purposes. Some are breeding to recreate the heritage breed. To me this is the hardest. Not only are they breeding for looks but for all of the other traits of the original breeds. That might be eggshell colors and shades, whether they go broody or not, and general temperament and behaviors for example.
Then you might have someone not worrying that much about the SOP but are breeding for enhanced egg laying or maybe for better meat production. Some are breeding to create their own breed or type, not looking to copy any SOP. Some people doing his are really good. Some not so much.
You have people that have no idea what an SOP is but get some hatchery birds and breed them. Some don't even understand that the father contributes genetics. I've seen posts on this forum where people were shocked the chicks did not look like the mothers and had no idea what the father looked like.
Of course, you have people in between all of these.
One complaint about puppy mills is that the pups are often inbred. Major hatcheries and many responsible breeders have certain techniques to maintain genetic diversity. Their livelihood depends on it. The pen breeding method works pretty well for hatcheries, especially if their breeding flocks are large. Many breeders use the line breeding method to develop their line which limits genetic diversity but once the line is established they may use the spiral breeding method to maintain genetic diversity. This is more tricky but if they know what they are doing they can maintain adequate genetic diversity for many many generations.
Are their chickens poorly bred or cared for?
When you ask this you need to define what you mean by poorly bred. Are you likely to win any grand champions at a major chicken show with hatchery birds? No, not really. But that does not mean that they are inbred like you might get at a puppy mill. They are designed to make a good product for a certain market.
