I mean, you're removing part of a living animal for human convenience. If the ethical issue isn't obvious I don't know what to tell you.
The practice has been banned in the UK for almost 20 years, under the exact same laws as ban declawing cats. It's unnecessary mutilation with no medical justification.
We neuter male cats so they don’t spray piss everywhere and spay female cats so they don’t go into heat and scream incessantly to be let outside.
Both procedures seem slightly more invasive than removing a scent gland in a skunk, given that it removes the sex organs that secrete hormones and changes their behavior for the rest of their life.
It’s possible that a skunk gets anxious when it tries to spray and nothing comes out, I can’t say I’m an expert in skunk behavior, it just seems less invasive than spaying or neutering to me.
We do a lot of bad things to animals for human convenience. Including forced breeding and raising them to be slaughtered.
The ethics is murky to me because I assume the procedure doesn't cause lasting pain and allows the animals to be pampered pets. The alternative is they are kept wild.