The shiftPWM does not use multiplexing but it requires a lot of refreshing to maintain the brightness level of the LED.
Do you need to control the brightness or are you going to just control on and off?
Controlling brightness AND multiplexing a matrix is possible but even more CPU intensive.
This is what you need to do for a multiplexed matrix.
http://www.thebox.myzen.co.uk/Workshop/LED_Matrix.html