In hall sensor based BLDC motor, motor is controlled by feedback of hall sensor. At a time only 2 stator pole pairs will be excited and 3rd pair will be ideal. So in third pair Back EMF will be generated. In my opinion we don't need that back EMF. So how that Back EMF is dealt with or reduced? Do they use Flyback diodes on motor? Or that Back EMF is used in any other operation?
Back EMF is always generated any time the rotor is moving. The back EMF for the phase wire that is not being driven can just be ignored if you are doing 6 step commutation with hall sensors. The part of the H-bridge connected to that phase wire will have top and bottom fet off so no current will flow, and the back EMF sees an open circuit.
The magnitude of the back EMF can be approximated using the Kv rating of the motor. For example a Kv of 50 means 50 rpm / Volt. So if a motor with Kv of 50 is rotating at 1000 RPM, the back EMF will be around 20V. If the battery voltage is over 20V, then no current will flow. If the battery voltage is less than 20V, then the motor will go into regeneration and current will flow through the body diode of the MOSFET (or whatever).
Generally, this only happens if the motor is being overhauled by the mechanical load (in other words, something externally is trying to make the motor spin faster... like an EV going down a hill or something).