How do we reduce or nullify the back current from the wheel motors of the modern electric vehicles?
As expected, this EMF opposes the voltage of the source that created it; that is, the motor becomes a generator as soon as it is turned on ...


Not quite. It becomes a generator when it starts turning. 


  ... and the opposing (or counter, or back) EMF will increase with increasing frequency.


With increasing rotational speed might be a better way of saying it.


  However, the applied EMF overcomes this "reverse emf" and makes the current flow in the direction suggested by the applied EMF; 


In normal driving the back EMF will always be less than the applied EMF as there is always at least a small load on the motor.


  ... in effect, the reverse EMF acts as a brake on incoming current and limits it.


Yes. Remember that the starting current for most motors is very high because there is no back EMF and severe heating is a result. Large motors may have a limit on how frequently they can be started (n times per hour).


  Won't it affect it affect the efficiency of the EV's. 


No. The motor controller applies the voltage required to generate the power required.


  Moreover if we where about[?] won't these back EMF badly affect the electronic circuit system.


The biggest problem with back EMF is in regenerative braking. If the incoming energy isn't fed back into the batteries then the DC bus voltage could rise to the point of damaging the electronics. If this is going to be a problem then a bleed resistor is used to burn off some energy to maintain the DC bus voltage at the designed level.

Back EMF is good. It reduces the motor current as it approaches the no-load speed determined by the applied voltage.