It's because of IDE hard drives, you could have two on the same ribbon cable, named "master" and "slave."

Edit: I always assumed there was a technical reason for why IDE hard drives use "master" and "slave"; IE, if the master used older versions of the IDE protocol it could slow down the slave, or that the master had some priority on the bus. Specifically, if "1" and "2" or "primary" and "secondary" were designations instead, it might omit some kind of detail that was important to whoever picked those names.