To answer your question, let's agree that in the motto, "You can't judge a book by its cover," the "book" refers to the true inner person while "its cover" refers to the person's external appearance. With that definition in place, Twelfth Night deals with Viola who covers her book as a male page and enters the service of Orsino. Countess Olivia, the object of Orsino's devotion, falls in love with the "youth" in the goodly cover. Malvolio is maliciously tricked into changing his cover for one of a fool. Viola falls in love with Orsino's cover even though his book is in love with someone else and is tempestuous on top of it.
Sonnet 130 talks about the cover of the speaker's beloved, suggesting that she has no qualities to inspire poetry from her wiry hair to her heavy walk. Shakespeare then writes that she is wholly beloved despite having a less than poetical cover. Twelfth Night exemplifies the motto quoted above and Sonnet 130 states the truth of the motto in one specific instance.