Yes, you can connect unused I/O pins to VCC or ground through a 0 Ohm resistor in Altera® devices. You need to consult the Quartus® II software .pin file for proper pin connectivity. Any of the unused pins that the Quartus II software .pin file says to connect to VCC or ground can be connected through a 0 Ohm resistor. Ensure that your board level connection does not conflict with any "reserve pin" option that you have applied for your project. For example, do not set "Outputs Driving GND" to the pins connected to VCC on the board.
Connecting unused pins to VCC or ground through a 0 Ohm resistor is beneficial for boards where the unused pins might be used for a later project (on the same board). This will eliminate a need for a total board respin in order to use these pins at a later time.