Ive heard theories about how it could possibly cause a problem by frying the joystick port or some circuitry, but I know plenty of people who use them and I've never heard of it actually causing a problem. I suspect that 99% of the time it's safe.
I keep one around but personally never use it because pads suck. I like real joysticks with a stick. I only have the pad because it came with an A2000 I bought and some people prefer pads (though I have no idea why).
