I wrote this in response to an information request on scaleless reptiles a while ago on a different forum.
Warning: This is long, but I feel a scientific literature review was warranted given the debate surrounding scalelessness in ball pythons. I have no conflict of interest in writing this report and no stake in the scaleless market other than finding scaleless animals fascinating (I own a scaleless Texas rat snake - a new acquisition). The too-long-didn't-read summary is at the bottom above the citations.
The genetics of scalelessness in reptiles is fairly well understood, as is scalelessness in birds (particularly chickens), and hairlessness in mammals (hair and fur are basically highly modified scales). It is known that the skin of a scaleless snake lacks beta-keratin (Citation A: see below).
There is scientific literature examining scaleless reptiles since the 1970s, including numerous studies examining their health in regards to water loss (no difference in northern watersnakes, citation B), mechanical resistance to the skin (reduced in scalelessness, citation B), heat transfer (no difference between scaleless and scaled gopher snakes, citation C). For more papers, feel free to search Google Scholar, although many articles may be behind a pay wall.
There is no documentation I know of that shows that scalelessness in reptiles is linked with other defects that could cause negative health effects or death. Instead, more data is available to show that scalelessness largely has no effect on the physiology of the animal. Scalelessness also does not cause negative effects in birds (except at low temperatures, which is to be expected for an endothermic creature, Citation D) or mammals (numerous examples exist), which have common ancestors with reptiles and likely inherited the scaleless/hairless gene rather early on in the evolutionary tree. Therefore, there is no evidence I am aware of that should make us suspect that scalelessness in ball pythons should lead to reduced health or death. If scalelessness causes physiological problems in ball pythons, that would be rather new knowledge in the scientific community, and certainly warrants close examination and peer-reviewed publication(s).
TLDR; There is no scientific reason for us to suspect that scalelessness in ball pythons is a deleterious (aka bad) trait.
Citation A: Toni, M. and L. Alibardi. 2007. Soft epidermis of a scaleless snake lacks beta-keratin. European Journal of Histochemistry 51:145-151. Available here:
http://ejh.it/index.php/ejh/article/viewFile/1136/1257
Citation B: Bennett, A.F., and P. Licht. 1975. Evaporative water loss in scaleless snakes. Comparative Biochemistry and Physiology Part A: Physiology 52:213-215. Available here: Evaporative water loss in scaleless snakes
Citation C: Licht, P. and A.F. Bennett. 1972. A scaleless snake: tests of the role of reptilian scales in water loss and heat transfer. Copeia 4:702-707. Available here:
http://compphys.bio.uci.edu/bennett/pubs/4.pdf
Citation D: Somes, R.G. Jr., and S. Johnson. 1980. The effect of the scaleless gene, sc, on growth performance and carcass composition of broilers [chickens]. Poultry Science 61:414-423. Available here: The Effect of the Scaleless Gene, sc, on Growth Performance and Carcass Composition of Broilers