Jane Austen arguably applauds self-discovery, by showing the self-discoveries of various characters in the novel.
Emma's own self-discovery is that she is in fact in love with Mr Knightley, and as this essentially results in a "happy ending" for both characters, it could be interpreted (as cliche as this may sound), that following one's heart is the key to happiness. On the other hand, Emma's self-deception would be her convincing herself that she was in love with Frank Churchill. Austen shows that (sorry for being cliche again) being honest with oneself is results in happiness. Emma is possibly the primary example of this.
However, Harriet Smith is also a character who deceives herself, or lets herself be deceived initially. Although at first willing to accept the proposal of Robert Martin, she later believes that she can 'do better' than Mr Martin (with the advice of Emma, of course). With the encouragement of Emma, Harriet pursues Mr Elton, and attempts to gain his affections. This could be interpreted as self-deception, as Harriet convinces herself that she has feelings for Mr Elton. However, by the end of the novel, Harriet discovers that she loved Mr Martin all along, and was possibly only influenced by Emma into believing she was in love with another.