Don't judge a book by its cover, right? The Witches sends us mixed messages in this regard. On the one hand, our main character turns into a mouse, but he's still the same great guy he always was and his Grandmamma still loves him. His looks don't matter much. On the other hand, the terrifying, ugly appearance of the witches reflects their terrifying, ugly personalities. Their looks do matter – so much, in fact, that they have to wear disguises to look like normal women. Either way, it's very clear that appearances – how people look – are very important in this book, for better or for worse.
They're pretty cool, but the illustrations in the book make it impossible for us to come up with our own ideas of what the characters look like.
We can't judge the witches' appearance the same way we judge normal women, because they're not even human. Maybe the witches are beautiful for their own species.