Just going to put in that the short legged mutation shows up in feral populations, and seems to actually be beneficial in some way amid some groups given the prevalence of the mutation. The reason doxies have back issues is laid out here (the same disease can happen in other breeds):
http://myminidoxie.com/dachshund-health-and-safety/why-do-some-dachshunds-have-back-problems/
As you can read, the form of chondrodystorphy in dachshunds (accounts for dwarfism) is what causes calcification.
Munchkin cats do not suffer from this same calcification link. Scottish folds however, have problems with osteochondrodystrophy, including calcification. I have seen recent trends in breeding munchkins to other rare breeds, and Scottish folds are among this list (Persians are more commonly added to the mix, the result being called a 'Napoleon' cat). Breeding to an unusually large breed or cats with links to health issues such as Scottish folds mean that what you are looking at isn't a 'munchkin', it is a cat with the munchkin mutation....plus other mutations.
http://mro.massey.ac.nz/bitstream/handle/10179/800/2whole.pdf?sequence=2 (Scroll down to page 175...going by the actual page numbers written in the bottom corner, not by the computer numbering) shows a chart comparing the many different forms of chondrodystorphy. Munchkins show up in a different grouping than, say, Siamese. As you can see, the axial skeleton is not affected.
Some people confuse so called 'twisty cats' (front legs shorter than hind legs) with munchkins. Totally different mutation. I'm sure most have seen cats with extra toes (polydactyl). This is a mild mutation, but the same gene can cause radial hypoplasia (ie. twisty cats).
Basically, I have not actually seen any solid evidence that Munchkin cats have any more spinal or mobility issues than other cats (lines with Scottish fold etc. bred in excluded).