You can check general purpose flag to test if the zip file is encrypted. Example function below.

<?php

/**
 * Check if the file is encrypted
 * 
 * Notice: if file doesn't exists or cannot be opened, function
 * also return false.
 * 
 * @param string $pathToArchive
 * @return boolean return true if file is encrypted
 */
function isEncryptedZip( $pathToArchive ) {
    $fp = @fopen( $pathToArchive, 'r' );
    $encrypted = false;
    if ( $fp && fseek( $fp, 6 ) == 0 ) {
        $string = fread( $fp, 2 );
        if ( false !== $string ) {
            $data = unpack("vgeneral", $string);
            $encrypted = $data[ 'general' ] & 0x01 ? true : false;
        }
        fclose( $fp );
    }
    return $encrypted;
}