First, no, we're not required to use the Attack 3 joysticks to drive the robot - think of them as a "starter kit" for rookie teams to begin driving. Many teams use other controllers, like Logitech gamepads or F310s (?), even Xbox controllers (see Killer Bees, FRC33).
As to the second, I don't know of any specific Apple app designed for driving FRC robots in a competition environment. Teams have, however, developed their own apps for related purposes. Devil Dogs (FRC441) used an iPad for their
targeting control in 2012. I believe MorTorq (FRC1515) also used something similar that year.