Yes and no. Munchkin cats are dwarf cats: normally pedigree cats with short legs and normal bodies. The dog equivalent is the Dachshund. This dwarfism in companion animals is caused by an inherited dominant, genetic mutation. Mutations occur all the time in nature which is why humans evolved. Genetic mutations are entirely natural. On the basis that mutations causing dwarfism are natural Munchkin cats are natural too.
However, if you believe in Darwin’s theory of natural selection you might argue that Munchkin cats are unnatural. This is because his theory of evolution – natural selection – is that slight variations due to genetic mutations are preserved if useful to the survival of the species.
It is not useful for a cat to have shorter legs than normal. Therefore in nature, in the wild, the dwarf cat (as a race of cats) would probably not survive. In which case the breed would die out. Natural selection would have removed the cat from the planet. The only reason why they exist is because breeders created them and sold them. On this basis Munchkin cats are an unnatural human creation made for human entertainment and company to meet the demand for cats with baby or cute appearances.
There is a third point to make. The short legs of Munchkin cats and all the dwarf cat breeds of which there are many serve no purpose other than to make the cats looks cute and attractive to humans. By contrast Dachshund dogs which are also created by breeders serve a utilitarian purpose. They are short-legged terriers. They are sausage shaped so they can go to earth, enter burrows. This makes the breeding of these dogs more natural in a human world.
Although I like Dachshunds I dislike the purpose for which they were originally bred. In the wild, as per dwarf cats above, the Dachshund would not have survived either because short legs are a disadvantage above ground where the dog lives.
SOME MORE ON DWARF CATS: