Whenever line breeding occurs, deleterious mutations are going to build up in the offspring. It is why, for example, purebred dogs have so many issues. In order to produce a particular phenotype, in some instances it is required to line breed animals. If it is a polygenic trait, then line breeding becomes almost a necessity. However, with ball pythons, every base morph is a single gene trait (unlike leopard geckos). Now there have been instances in which the gene producing a morph is also linked (either pleiotropically or due to linkage disequilibriums in the chromosome) to a defect. These are the examples that Tosha has mentioned.
What this means is that line breeding is NOT a necessity when producing particular morphs. Does it occur? Yes, it is quite common but it is not essential to line breed in order to produce it. I don't see any build-up of defects occurring in morphs unless a) the defect is specifically associated with the gene producing the morph (which we have already seen) or b) breeders line breed their animals to excess. If scenario b) does occur, it will always be possible to outbreed morphs and eventually produce morphs without the defects.
In short, genetic defects do show up in morphs, but there likely won't be the same plethora of problems seen in animals with polygenic phenotypes (dogs, cats, mice, etc).
