The nozzle exit diameter is used to calculate the nozzle exit area, which is used in the power-on drag coefficient (CD) calculations, and to vary thrust with altitude. With the nozzle exit diameter entered you will see two CD curves, power-off (coast) and power-on (thrusting). If you have a large nozzle exit diameter, filling the base area of the rocket, there will be a significant reduction in the power-on CD. If your rocket gains a significant amount of altitude during the motor burn, or is an upper stage ignited at high altitude, there will be a noticeable increase in thrust at altitude compared to the rasp motor data.
That said, these effects are very small for a small nozzle exit diameter on a low altitude model or very low end high power rocket, and can be ignored. As noted, you can leave the entry line blank, and RASAero II will assume a nozzle exit diameter of zero. CD power-on will equal CD power-off, and there will be no variation of thrust with altitude.
Chuck Rogers
Rogers Aeroscience