Its always a good idea to have caps installed on your motor even if Novak says you don't need them. With the motors that have surface mounted caps, just leave them there. It won't hurt anything.
For the diode I assume you mean the schotky diode on the motor. This diode helps keep the ESC cooler and gives you more consistant brakes (especially in mod). Just pay attention to the proper polarity because if you connect it backwards it will blow.