The received wisdom is that clipping into your pedals results in a 30% efficiency saving as you can apply power through more of the pedal stroke, and pull up on the pedals too. This isn't something that's been borne out by science, but there is definitely some performance advantage from clipping in, particularly at higher power outputs (think sprinting). If you're aiming to go fast then clipping in will help, but otherwise flat pedals won't hold you back in any real sense.