In the books yen uses magic to hide her hunchback and ugliness. Geralt being a Witcher and therefore trained/experienced to analyse magic in front of him quickly sees through the illusion. If the show had the character look uglier to begin with then that's probably a result of adapting the books. I haven't watched the show as I don't really like adaptations. Btw it's not just Yen that uses magic to hide ugliness either, almost all other sorceresses do as well in the books including Triss.