remove_unused_shortcodes.php

<?php
add_filter( 'the_content', 'strip_usless_shortcodes', 50 );
function strip_usless_shortcodes( $content ) {
	preg_match_all( '@\[([^<>&/\[\]\x00-\x20=]++)@', $content, $matches );
	$pattern = get_shortcode_regex( $matches[1] );

	$content = preg_replace_callback( "/$pattern/", 'strip_usless_shortcodes_callback', $content );

	$content = str_replace( '<p></p>', '', $content );
	return $content;
}

function strip_usless_shortcodes_callback( $matches ) {
	return $matches[5];
}