Many animals don't -seem- to suffer. Snakes especially will not allow a single hint of pain to show due to their extreme survival skills and their inability to express many things in a manner which we will understand. Fact is, you don't know.
By that logic even the pure cornsnakes we have in little sweater boxes or 75 gal aquariums may be suffering, too. I don't see that stopping anyone from getting more snakes. So, in essence, neither of us knows if any snake in captivity is suffering, where they're pure or not.
Within nature- you have natural selection to "weed out" those who cannot survive. In your home- you take this major factor away. You can assume all you want that a said specimen will or will not survive in the wild- but it remains an assumption because you cannot and shall not imitate a totally natural environment to see if he dies or not.
It is taking a chance, and you won't be the one who ends up paying for your mistake but they will.
Are we breeding these animals to release them into the wild? No. We aren't trying to save a species and repopulate natural habitats. We're breeding pretty snakes. If you find a vet who has studied, and concurs, with your theory, then I will take it more seriously. Until then, we can only go by what we experience and I haven't had a single vet tell me my snakes are suffering from cross breeding. So again, neither of us knows for certain.
Personally I think too many assumptions are made without really testing them out. It is far more comfortable to think that the snakes are fine because they -seem- fine, but in truth they may be suffering.
Just like many dogs who are very happy and seem totally healthy, but in truth will suffer from leg/waist/jaw pains when they get older.
And so do wolves and lions and tigers and elephants and deer and any other wild animal you want to mention. They don't just go merrily along, healthy as the proverbial horse, and suddenly keel over and die. Their bodies get old, they get arthritic, they get cancer, they get a myriad of other problems that humans had no hand in.
Dogs today suffer from ailments due to our selective breeding- whoever think that snakes won't end up suffering from the same fate is delusional at best, in my opinion. It is the same process, it is evolution which is condensed into unnatural environments and terms, which heeds to rules which have little in common with the that apply in the wild. I don't think you should expect different results a few generations hence, as as I said before- again it won't be us who pay the price.
I still don't see you giving up your snakes, although they may have been inbred. Who knows whether they were or not? We're each in this for our own reasons. I am well aware of potential pitfalls when crossing genes and playing God. Humans do that every day in everything that we do. Are we headed for disaster? At some point we will probably destroy the planet through global warming and other lovely side effects to our experiments and lifestyle. Do I think that we are risking the suffering of snakes by hybridizing them? No. Not at all. I want proof. It's that simple. Theorizing only goes so far for me. You ahve your belief and I have mine. I think we can get by on that.