You could use a digital pin (+ something more) if you just want to turn the motor on / of, but this would not allow you to control the speed or direction af the motor. You would al least need to control direction since the faders must be able to go both up and down.
Using two output pins allows direction. Speed requires PWM though.
If so, can I use 48 motorized faders (meaning 48 motors) in a single arduino?
You'll need something else to control the motors. A Arduino cant handle that kind of current. Google around for various motor controllers. Then use something like a 595 to allow the Arduino to control that many motor controllers.
if I were to program it in assembly, but I think that would mean I would have to get a new programmer.
A) Said programmer is only 4 resistors or so. B) C is translated to a .hex file and then transfered. Assembly is processed the same way. You'd just need to figure out the right commands to use assembly.
Slower animation which you'll be wanting is dead simple with the Arduino.
I'd use the MAX7921. It drives a 8x8 grid so if you want bigger you just hook more up together (they only need one set of pins). Its also rather light on the battery because only one LED is on at any time yet it still looks good.