My 'sonas wear clothes mostly to express their personalities and it feels more "normal" to me. Although Katsuro does go around shirtless sometimes.
Kyro usually doesn't wear clothes, but she will occasionally.
Raven wears clothes pretty much all the time. It makes her look cuter anyway.
Foxi normally wears clothes, but on occasion she won't wear a shirt. Even though she's a female, she has floof to "conceal" herself. But mentally she doesn't care about acting terribly female-ish.
Karasu is a feral, so she never wears anything.
Dusk just wears a brown collar, since she's basically just a wild Pokémon who acts more domestic.
I'm in the process of making a deer and a German shepherd, so they don't even exist yet.