My Magic Aire Unit Ventilator has field provided DDC Controls with a factory provided ECM Motor. Is there any problem shutting the unit off and on by its line voltage?

Yes.  The ECM Motor has large capacitors in the electronics section.  When the incoming power is cycled on/off, these capacitors are stressed. Starting and Stopping the motor by engaging/disengaging line voltage will significantly reduce the life of the motor.  The proper way to start/stop the motor is to break the 24V control supply to the motor.

Where do I find the part number for a replacement motor capacitor?

All replacement motors are received with the capacitor as part of the motor.  Capacitors are not available seperately.