Use a extensão joliet e você deve obter os nomes reais dos arquivos.
mkisofs -J -o cd_image.iso /directory
Da wikipedia:
Joliet is the name of an extension to the ISO 9660 file system. It has been specified and endorsed by Microsoft and has been supported by all versions of its Windows OS since Windows 95 and Windows NT[citation needed]. Its primary focus is the relaxation of the filename restrictions inherent with full ISO 9660 compliance.