If nature was to take its place, not every male would be able to breed and among those who do, not every male gets to sire their offspring (ie sperm competition, the arms race against the female sex organ defenses, etc). We used to think the larger, dominant male of a species typically gets mating rights and sire the group's offspring. Come to find out, many of the smaller, submissive males plus the willingness of some promiscuous females sire the offspring that are reared and/or protected by the dominant male (Unknown to him). Females generally have a lot to say in deciding who to mate, and even after the fact, whose sperm to reject or keep.
So if we were to let nature be for our snakes, how can we meet that goal? In the wild, numerous males compete for the one female. In captivity, are we allowing our males to fight to breed? Even if there is a victor, it is still selective breeding because the victor came from a very small pool of males vs a random, large sample of males.
If a population grows too large to support itself, breeding should halt, whether it be in captivity or in the wild. Specifically for captive bred ball pythons and bearded dragons, there are way too many being hatched and not equally good homes provided to each one. Craigslist is a constant reminder of the abundant and unwanted.
So breed if you will, but breed responsibly with the plan of ensuring each one you bring to their world goes to a proper home.
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