Why my first new WP_Customize_Image_Control doesn’t work

The second argument for WP_Customize_Image_Control is the ID of the control. You’ve given the same id to both image controls, 'Agmor Bootstrap'.

Give them unique IDs and both should appear. Using the name of the setting is a simple option:

new WP_Customize_Image_Control($wp_customize, 'header_logo', array(

new WP_Customize_Image_Control($wp_customize, 'header_background', array(