I personally think that animal breeding is best when it goes in different directions that the one it is going with such morphs as scaleless.
That said, this isn't an isolated or new issue. OP, you mention certain dog breeds as analogous, but probably many more are relevant -- all the breeds that are at increased risk of hip dysplasia, and the herding/working breeds that perhaps shouldn't be on the pet market.
Livestock breeds are the same. Wool sheep breeds need a lot of extra care to live -- wool is a selectively bred trait, and does not benefit the sheep. Without regular shearing, wool sheep are at high risk from overheating (especially during lambing), makes them a lot more susceptible to flystrike, and since their tail doesn't stay clean of feces as it does in wild coat type breeds it is almost always docked (cut off) shortly after birth. What's somewhat worse is that these breeds are still currently used for meat even though the wool isn't worth the cost to shear it.
Cornish Rock chickens (a breed cross used for virtually all chicken meat in the US) are much more troubling than any problematic reptile morphs. They grow ridiculously quickly (broiler chickens in the store were harvested at 7 weeks old) and so cannot be provided perches (their underdeveloped legs break when they hop down in the morning) and cannot be fed free choice (they will literally eat themselves to death). At harvest, their organs look terrible -- swollen and discolored. Of all the chicken breeds I've kept (six or eight over the years), Cornish Rock are the only ones I think shouldn't exist.
In all these cases, there are real or perceived financial incentives to keep producing animals whose morphology detracts from their quality of life (either directly or because they tend not to get all the additional care they need). I wonder: if all reptile morphs of a certain species had the same price tag -- that is, remove the profit motive from breeding, and the Veblen Good motive from buyers -- which morphs would people breed?
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