I see that my Arduino MEGA2560 card has 15 PWM outputs which can control five stepper motors with microstepper.
So, I am asking; is that enough with three PWM outputs for each stepper motor ?
Can the arduino card control three PWM outputs in each clock cycles ?
You don't need any PWM outputs to drive a stepper motor. You need a stepper motor driver such as a Pololu A4988 which just needs 2 connections to the Arduino for direction and step signals.
All the complicated stuff is done by the stepper driver.