For me it's just about genetics, and the fact that I think humans have a responsibility to limit their intervention with other species. By taking a snake out of nature and putting it in a box in your herp room, you're doing something really abnormal to that individual animal. It's life is never going to be anything like it would have been before you, or the person who removed its parent / grand-parent from nature, intervened. But it's still just an individual animal.
All snakes have a common genetic ancestor from which they have moved further and further over millions of years: adders and Stimson's have been separated for so long one would have the other for lunch rather than breed with it, but according to current theory on subspecies, Children's and Stimson's haven't been apart that long yet. They're moving very slowly but very steadily in that direction. One day, they'll be completely speciated and no longer able to interbreed. By cross breeding subspecies or localities, you're throwing yourself into the middle of that process, essentially looking at hundreds of thousands of years of evolution differentiating those two snakes from one another and saying, for one moment in your puny little human life, "Nah, stuff it!"
In my opinion, it's the absolute height of arrogance for a human to think they're smart enough to improve on what nature is doing and has done, and to intervene with other animals not just at an individual level, which is questionable enough, but at a species level. Look at chihuahuas and puggs. Their ancestors would eat them for lunch, but a wolf wasn't good enough for humans, we wanted something little and profoundly stupid, and fifteen thousand years later: voila. As far as I'm concerned, the average solitary pugg's life with constant respiratory problems and canned food doesn't compare to that of a wolf with its pack in the wild. The wolf might not be food secure or get doggy treats when he rolls over, but damn, at least he's living a normal life. In the same way, assuming we don't cook the planet or blow ourselves to Kingdom come first, a few thousand years of selective breeding in snakes and god only knows what pointless creatures we'll produce with what defects from systemic inbreeding. It doesn't bear thinking about.