In the book You Are Not So Smart, are heuristics helpful or harmful or both?

Keep in mind that heuristics are methods or techniques that McRaney calls "mental shortcuts you use to solve common problems."  Also keep in mind that the full title of the book is as follows:  You are Not So Smart:  Why You Have Too Many Friends on Facebook, Why Your Memory is Mostly Fiction, and 46 Other Ways You're Deluding Yourself.  Understanding these two things clarifies the question a bit.  Your question is really about the techniques involved in our self-delusion.  

The three main subjects in this book are cognitive biases, heuristics, and logical fallacies.  These are components in your mind, like organs in your body, which under the best conditions serve you well.  Life, unfortunately, isn't always lived under the best conditions.  

This quotation contains the answer to your question.  McRaney admits here that heuristics do "serve you well," but only "under the best conditions."  Therefore, the answer to your question is that heuristics are both helpful and harmful.  
To clarify further, McRaney gives many examples.  As long as these human "self-deceptions" are "quantified by psychology" and known, then our techniques or heuristics are helpful because they "keep us sane."  However, when we continue to be self-deluded and believe our fantasies to be truth, they become harmful.  For example, these techniques or "mental shortcuts" can speed up the brain's processing (which is helpful), but sometimes make us "miss what is important" (which is harmful).  Arriving at any particular conclusion too fast is never good.  
McRaney gives a practical example about news stories featuring shark attacks.  If we see too many of these news stories, our "mental shortcuts" or heuristics tell us that evil sharks have become out of control and cannot be stopped.  This kind of fallacy is harmful.  However, if we can recognize that this is a self-deception, then we can realize that the only thing we really know is that the media is focusing more on sharks because this keeps their clientele interested.