Drop all tables belonging to the site during the deletion of the site on multisite.

drop-tables-ms.php

<?php

	/**
	 * Drop all tables belongs to site.
	 *
	 * @param array $tables  The tables to drop.
	 * @param int   $blog_id The site ID.
	 *
	 * @return array
	 */
	add_filter( 'wpmu_drop_tables', function ( $tables, $blog_id ) {
		global $wpdb;

		$site_tables = $wpdb->get_results( $wpdb->prepare( 'SHOW TABLES LIKE %s', $wpdb->esc_like( $wpdb->get_blog_prefix( $blog_id ) ) . '%' ), ARRAY_A );

		if ( ! empty( $site_tables ) ) {
			foreach ( $site_tables as $table_item ) {
				$table_item = array_values( $table_item );
				$tables[]   = $table_item[0];
			}
		}

		return $tables;
	}, 10, 2 );