It will depend partly upon how close you are to your opponent.
The foot has a greater potential velocity due to the greater arc it traverses en route to the opponent.
The shin has a lesser potential velocity, but is far more rigid than the foot, and perhaps less prone to damage than the top of the foot when making contact with a head.
The top of the ankle is reasonably robust in the context of head kicks, and provides a good 'middle ground', allowing for a margin of error both up and down the limb when gauging the range of your attack.
Successful execution of a roundhouse head kick will likely reap dividends regardless of whether contact is achieved via the foot, the top of ankle or the shin, and it is definitely worth incorporating each into your training regimen.
When kicking opponent's body or lower leg, the shin will often be more appropriate, depending upon the striker's skill level, conditioning, and the purpose of the kick.
This brief Fight Tips video provides supporting info and demonstration.