well, there would be a variety of ways it could cause a performance hit: in addition to memory, they could reduce your FPS if they are being moved around, or have behaviors that eat up CPU time, or are triggering collision checks.
Why would you need a lot of empty sprites? to hold data? You could store data other ways.
I know there are plenty of good reasons to use invisible sprites (I use them to track touch points in a multi-touch interface, or make larger targets around small objects that are otherwise difficult to touch on a small screen), but just make sure you use as few as necessary and keep them as simple as possible (no behaviors, disable collisions, etc.)