Most likely it is dependent on how the game was implemented.
From my experience, when developing a homebrew application you have to explicitly enable 3D mode on startup to have the stereoscopic view available and then access the position of the slider to determine the difference for rendering on the left and right screen. If you do the check and the slider is off you can do a trick such as "don't render anything on the right screen since it isn't rendered" but maybe some games don't bother with the check and just render both at all times.
