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My take on the issue comes down to general biology. Snakes have scales as a physiological defense against dehydration, predators, and the general environment. To take away something that is essentially "necessary for normal life function" is wrong. I feel that way about most genetically malformed creatures that we have tinkered with.
There is also a difference in something missing scales (which prevents to some extend normal bodily functions) and breeding something for say, color or pattern. I haven't seen many scaleless reptiles in person, but the few I have seen have chronic fungal or bacterial infections / chronic dehydration issues / retained shed etc. I also work at a vet clinic so I am not always seeing the healthy pets.
The two that come to mind with stuck shed were certainly weird. It seemed that without the scales, the natural lubricant they produced didn't serve it's purpose normally. The old skin just adhered to the skin beneath, in a few thinner spots, like just behind the jaw and around the vent, the new skin actually tore when the old skin started peeling. Neither survived long. These were also corn snakes, but I would assume the effects would be similar. Their care wasn't terrible, humidity was a little too high for 'normal' corn snakes (breeder suggested higher humidity since they lacked scales) and they had red lamps with no thermostats, but compared to some husbandry, it wasn't awful - the owners had done more research than most.
I tend to believe that screwing with genetics for aesthetics purposes is almost always a mistake. This starts to get into the immoral (and at times cruel) side of things when you are selective breeding for things that are so detrimental to basic biology that the animal can't preform 'normal' activities. The animal may not seem unhappy, but that does not mean that it is ok.
To me, a scaleless reptile seems as twisted and unnatural as say, a skinless cat...The only difference is the skinless cat would die very quickly from fluid loss, so no one would breed them.
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More thoughts...
I know everyone mentions various dog breeds, but this also has a valid point. To me there is a difference in continuing to breed brachycephalic animals that literally exist in a state of hypoxia because their nose and/or soft pallet are abnormal, and breeding dogs that (usually) are only a certain color +/- some other possible congenital issues. Labs are predisposed to hip dysplasia and lipoma's, but the grand majority function, (breath / breed / run / eat) as a normal dog should. There is no such thing as a 'normal functioning' french bull dog. Sure a frenchie can run and play and enjoy car rides, but that 'cute' snuffling snort is not breathing, it's their soft palate getting in the way of their trachea - with every breath in the soft tissue sucks against the windpipe like putting your finger over the bottom of a straw, they literally can't take a normal breath. This is not always severe, but we see a lot of dogs that need surgery to cut this tissue out (usually done when they are spayed or neutered around 6 month - 1 year old). The surgery can greatly improve their quality of life. But is is right, or moral, to purposefully breed an animal that will need corrective surgery as a puppy just to breath somewhat better?
The moral issue comes into play when people start looking at something that they have created and weigh the "having to take extra steps to care for x" against the quality of life of said organism. We joke at work that when doing surgery on brachycephalic breeds (cat and dog), they should be done last since they take so much longer to extubate (wake up from anesthesia). Which they do. Most animals start to swallow and gag as soon as they wake up enough to feel the endotracheal tube that is protecting their airway. 90% of the time, the flat-faced breeds don't fight it, some even just resting and looking around with the tube still in - as if their body is like "wow, so this is what air feels like".
If someone can justify the cost and extra care a genetic mess of an animal needs against the animals' quality of life, then you will likely find a market for those animals. And once money gets involved, suddenly quality of life takes a back seat to profit (not just on the breeders. If people didn't buy these breeds then no one would sell them). Pet owners that have a bull dog that is doing its best to be a dog will see a happy, lovable dog that enjoys life as much as anything else. That animal does not know any other way of life - so if it is not actively suffering pain or distress, does it have a good quality of life?
Is it immoral to breed animals that have genetic issues because they can't perceive any other way of life? The animal does not know that it is not as nature intended, they just live.
A kitten that is born blind from some fluke will grow up to be a perfectly happy and normal cat that acts like any other cat. Some owner would come along and make allowances and do everything possible to give them a great life. That's wonderful and nothing is wrong with that. They'd learn their owners schedule and would play, purr when being petted, beg when they heard the food bowl, etc
But...
What if someone came up with a mutation that caused abnormally large but non-functional eyes - just because things with big eyes are cute? Large eyes are more prone to ulcers and injury, esp if they are non-functional. Sure there are medications that could heal the ulcers, eye drops to keep the cornea's healthy, etc. These big-eye'd cats would also live as happily as any other, they'd purr and play with their owners, beg for food, and play in boxes too. But this, to me, would be very immoral and sad.
Sorry for the very long winded post
I am not trying to attack or judge anyone that has any of the breeds mentioned in this post. This is more of a philosophical discussion of morals and animal husbandry
I myself have a ranchu goldfish, which is essentially the "pug" of the fish world (fat head, round body, no dorsal fin), and I know that he has special needs beyond any regular classic goldfish. But I really had to ask myself whether I could have one given how I feel about selective breeding for aesthetics. My ball python is also a Cinnamon Mojave, not a "normal", so genetic tinkering made him too. So to that point, I'm also a hypocrite.
 No cage is too large - nature is the best template - a snoot can't be booped too much
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