Interesting points indeed. I think that malnutrition would have a considerable impact on the health and development of an animal, no matter the species.
I adopted a malnourished kitten from a coal mine over a year ago, and even before her untimely death (if I find the sucker who maimed her, I'll kill him) she still suffered from skeletal problems because of her poor nutrition when she was at a critical point in her growth.
I've seen malnourished breeder rodents that end up "hump-backed" and have bent limbs because the body robs the minerals it needs from it's own skeleton therby weakening the bones themselves.
The same is also true for humans deprived at a young age. Rickets and other skeletal abnormalities will surface when the minerals and vitamins aren't present in the diet when the body needs them the most.
Also, when a snake is malnourished I would tend to think that it weakens the bone structure and the supporting structures nearby. So when wild movement such as thrashing or being wrestled with by a cat, the spine would have the leeway to slip from its proper position, which under optimal conditions wouldn't normally happen. And if they did, it would take considerable force to move ths spine and would most likely result in death of the animal.
But it does seem like the logical conclusion for kinking after hatching, especially in those problematic feeders. Either they be non-feeders or feeders who tend to regurge often. And it also seems to explain the fact that once feeding properly on the highest quality food, the minorist of kinks all but disappear. I would assume under x-ray examination that skeletal scars would still be present, but due to the flesh and skin would be un-noticable by the naked eye.