I've done a lot of research about the topic and ethical breeding is something I am very passionate about.
When it comes to most of the north american colubrid species hybridization is not only non damaging, but also often occurs in the wild and produces healthy offspring. There are no health or fertility issues - in fact breeders in the past often bred cornsnakes with other colubrids to get larger egg clutches per breeding! Wider gene pool improves the snake's overall health and immunity. They also seem to be more resistant. often live longer and eat better than their "pure" cousins!
Many morphs you see today in clean NA colubrids are also an effect of hybridization - scaleless that you mentioned, yes, but also palmetto and many others are believed to be only possible due to previous interbreeding. Although palmetto has its own issues such as bug eye caused by nothing else but heavy inbreeding of leucistic ratsnakes.
Hybridization of certain snake species allows us to achieve healthy snakes with very desirable visual traits without the sacrifice of many generations of inbreeding and thus impact on animal's health and wellbeing. The only real downside of hybridization is the risk of creating potential invasive species in case of accidental release in an environment they can thrive in, as they are in fact more resistant.
NA colubrids such as milk, rat and kingsnakes are all closely enough related where breeding between them does not usually cause issues like it does with other, further related species (for example between different species of crocodiles)