Why attack aircraft strafed anti-aircraft gun crews

Did Japanese aircraft deliberately strafe anti-aircraft crews before dropping armor-piercing bombs?

Yes, but the tactic was not uniquely Japanese; British and American aircraft also used strafing to suppress defenses before the main attack.

British and American aircraft also used machine guns and other weapons to suppress anti-aircraft defenses before attacking. The aim was to reduce the fire coming back at the attackers. The Enterprise example raised in the question concerns reported shrapnel casualties among gun crews; it does not establish that strafing caused those casualties.