USB joysticks can be slower if there's other traffick the USB controller has to handle. Old fashioned PC joystick are being dealt with the interrupt request of the sound card, which means the CPU is interrupts it's tasks immediately to do the sound card tasks (among sound, the reading of the joystick status). That is, if we're talking DOS, not Windows as the latter has an hardware abstraction layer, and I don't know much about the implementation of that.
With the Amiga, not the CPU, but one of the custom chips (was it Paula?) is being interrupted to do the joystick handling. So, strictly spoken, it should be faster, yes.
But whether you'll notice in reality, it depends on what kind of pc you have and what kind of software you're running.
