The superclocked versions normally are factory overclocked, and have a better cooling system. Yes you could probably overclock the standard to superclock levels, but you will also be able to overclock the "superclock" one even more.
If it does have a better cooling system, I would go for the super clocked version. I have a MSI GTX 460 Hawk (one of the best coolers around) (a 560 is a heavily overclocked 460) and I have it overclocked to 900MHz, which is equal if not greater to the speed the"superoverclocked" 560's come shipped as. The extra cooling ability makes a huge difference in the amount you can overclock.
Edit: Are you looking at two specific cards, or just in general? Not all superclocked cards coolers are created equal, so don't just go buy the cheapest superclock card