A horrible accident while she was working as an intern at a small office in Manehatten, involving an industrial 3-hole punch. It's only mentioned briefly in a flashback, but the fan theory is that that event is what turned her to evil.
You're being way too nice, and making me feel bad for lying to you.
The swiss-cheesiness of changelings is never addressed in the show. I suppose they just did it because it looks visually interesting, and it helps to further differentiate the changelings from ponies, making them more stranger and more foreign. I like my version better though.