If that person is close to you, of course you are going to say how you truly feel. I think there are variations of saying, ¨I´m fine, thank you.¨ If the person really feels saying that, he will smile while saying it. If there is something wrong, he will smirk or frown and say that in a downcast voice.
At least they know what you are feeling so they won´t get the idea that you´re being plastic.
But what if, the person who asked you "how are you" is one you haven't met for years. He approached you with a big smile and asked, "How are you, Mary Joe?"
Wouldn't you be considerate enough to tell him "I'm fine" and not showing all the wrinkles on your face or dropping on his shoulder and hollering with a loud "waaaaaah".