Afaik frame duping is a way for the emulator to match the refresh rate of the display by duplicating frames. So for example if a game runs at 20fps, the emulator would still output 60fps but just display every frame three times. It doesn't improve performance, it just helps with frame-pacing for a smoother experience.
Ok, then that explains the performance decrease when you turn this feature on and why it performs better with a higher clock speed while turned on.