Unused Stop Clock

Does the stop clock still exist in the game's data or was it only a sprite?

Presumably, this item functioned like the one in the original Zelda 1. The quack medallion functions similarly to that item, so that might just be the data.

Stop watch, Zelda's letter (an item which was planned to be needed to get the Mirror) and the Meat (substitute for more hearts with one pick up) were not used in the game. As far as I know only the gfx exists for these three.