The estop switch is actually a low-voltage input to Mach3 that tells the computer to shut things down. On my control board, it connects to a pair of pins on a 9-pin connector. The board then sends that info to the computer on the 'printer' cable that connects the two together.
In Mach3, this input can be configured to either normally open or normally closed by setting Active High or Active Low for the pin number.