You should use API plugin in order to remove default shortcodes. Use the filter called su/data/shortcodes.

Disabling all shortcodes

To remove all shortcodes, you should simply remove all elements from shortcode array.

add_filter( 'su/data/shortcodes', 'remove_su_shortcodes' );

/**
* Filter to modify original shortcodes data
*
* @param array $shortcodes Default shortcodes
* @return array Modified array
*/
function remove_su_shortcodes( $shortcodes ) {

// Remove all shortcodes
$shortcodes = array();

// Return modified data
return $shortcodes;

}

Disabling specific shortcodes

Use the same filter as in the previous example in order to remove specific shortcodes. However, not all elements of the array, but only some elements will be removed. For example:

add_filter( 'su/data/shortcodes', 'remove_su_shortcodes' );

/**
* Filter to modify original shortcodes data
*
* @param array $shortcodes Default shortcodes
* @return array Modified array
*/
function remove_su_shortcodes( $shortcodes ) {

// Remove button shortcode
unset( $shortcodes['button'] );

// Return modified data
return $shortcodes;

}