That will work, although you may have to adjust the LED series resistors to get the brightness you want.
One reason people usually do not use NPN transistors as "high side" switches is the drop of about 0.7 V from the transistor base to the emitter. The output voltage of a typical port pin is less than 5 V (the ATmega data sheet specifies the minimum value to be 4.2 V), so your LEDs are effectively powered by a source providing about 3.5 V.
An emitter follower has relatively high input impedance, so you don't need a resistor between the port pin and the transistor base.