I've been around ethical breeders most of my life and sometimes culling (by death) is the most rsponsible, and difficult thing a breeder ever has to do. In my experience it is never undertaken lightly, and many tears are shed.
Deaf puppies are particularly horrible as you don't know until they're 6 to 8 weeks old. Yes, they can be trained with hand signals, and yes they can make delightful pets, but a breeder knows that deaf puppy will need a special, dedicated owner, and those owners are not your average pet owner.
Culling because of color isn't as common anymore because of early neuter options, but it was once done to preserve breed type. I knew a boxer breeder in the 70s who PTS any white pups in her litters. I was horrified! She told me that the first time she had a white pup, she sold it as a pet that the owner was supposed to spay. Instead that puppy was used to breed intentional litters of white boxers, much to the breeder's dismay.
In todays "rare, designer breeds" atmosphere, placing puppies with color or marking faults is made more difficult by the advent of the new registries. A breeder can withhold papers, and insist on spay/neuter, but the CKC (or others) will register that dog if you pay the fee. Way to many "pet" buyers get the urge to breed, so often an ethical, caring breeder has to make hard decisions.