How do i remove the ‘WooCommerce’ section from Customizer in Twenty Sixteen Theme?

WooCommerce adds itself to the customizer as a “panel”, not a “section”.

Add this to your my_customize_register() function and it will be gone:

$wp_customize->remove_panel( 'woocommerce' );

References:

• woocommerce/includes/customizer/class-wc-shop-customizer.php line 31

As a rule of thumb, when you want to remove something (a customizer section, an action or filter, etc.) looking for how it is added in the first place is a good first step. More often than not it will point you in the right direction.
There are as many ways to remove things as there are to add them, and the right way to remove something often depends on how it was added.