On the one hand, although I’m always excited by the prospect of finding and encountering rare pokémon, I am uncomfortable with the concept of collecting pokémon in the way some pokémaniacs do. Pokémon, after all, are living, breathing creatures, and to reduce their value down to their pelt or skin color is a little … problematic.
On the other, if you’re referring to shiny specialists (those who are paid to find or breed shinies for others), rest assured that there’s more to it than that. Shiny pokémon sometimes struggle in the wild as noted here, so trainers who are hired to find and catch them through legitimate means (that is, by obeying capture laws and avoiding poaching) often focus on species whose shiny variations would fare much better in a domestic setting than in the wild.
Likewise, all reputable breeders require certification to run a day care, so those who run services to breed for shiny pokémon are required to rehome the non-shinies. Oftentimes, if you ask these day cares, you’ll find that they often either give their non-shiny pokémon to starter distribution centers or run sizable no-kill shelters themselves, which are often open to those who wish to find pets as well as partners for trainers’ journeys. (Breeders are barred from culling their hatchlings or releasing them en masse into the wild. Either are great ways of failing inspections and having licenses revoked.)
Of course, reputable trainers-for-hire or shiny breeders are few and far between, and the shiny enthusiast culture often encourages seedier practices, rather than the legitimate ones. All too often, I hear about a trainer who essentially poaches a shiny or a trainer who accepts eggs from non-specialist day cares, only to release non-shinies into the wild en masse (thus often disrupting the local ecosystem). These would be irresponsible, especially because they’re often coupled with the tendency to treat the shinies they obtain as trophies, rather than as living beings. It’s unfortunate that this happens, yes, and it’s not something I condone, even if the shiny in question is a particularly rare pokémon I would love to see.
Thus, to put it in short, I’m fine with the idea if you obtain your shinies through legitimate means or set up honest, humane businesses that follow strict ecologically-friendly policies. I’m less comfortable with the idea if you don’t intend on following humane, eco-friendly practices.