how to get one PWM more on MEGA!

Maybe it will find its way in the coming Version.

I guess the PWM for pin44 was forgotten in the actual release. if you add:

} else if (digitalPinToTimer(pin) == TIMER5C) {
            // connect pwm to pin on timer 5, channel B
            sbi(TCCR5A, COM5C1);
            // set pwm duty
            OCR5C = val;

to the wiring_analog.c the PWM will be executed on pin44.

if you know any other reason (except being forgotten) why it wasn't implemented, please let me know.

No why? So just forgotten?