Stefano,
Yes, you could use the PCI-6602 to control a stepper motor. This will require two counters per stepper axis to control the step/dir or CW/CCW lines, or one counter per axis if you only want to move in one direction. You would need to programmatically ramp up the pulse rate to control acceleration. However, since updating the output pulse train frequency is software timed, acceleration may not be very smooth and you risk losing step. Also, you would need to manually handle any pull in moves.
While you could achieve reasonable stepper control with the counter board with some trial and error, the PCI-7334 would probably be a better solution. This controller easily handles acceleration and deceleration and allows you to route the encoder signals over the
RTSI bus to control the data acquisition process.
Regards,
Brent Runnels
Applications Engineer
National Instruments