One is soft and one is hard. In one case you are you take away the power in case of an emergency,like shuting the whole machine down. In the soft case you are stopping the program using software which is not failproof.
FWIW, my estop takes the voltage away from the opto's, and when applied, all axis stop INSTANTLY, of course the program continues to run but there is no movemement of the axis.
RICH