Putting the speakers into enclosed slot or cubbies will definitely affect the sound, and not for the better. The further that speakers are away from nearby surfaces, the better they can sound, generally. By putting them in a shelved area, you increase diffraction effects which degrade the sound. You also greatly increase loading in low frequencies which can greatly boost bass thereby creating for muddy or boomy low end. The speakers' present positioning in the picture is pretty good as is.