Military ballots are handled through the military mail system. They are identifiable. In 2000 DemocRAT attorneys in Florida managed to disqualify military ballots because they were not postmarked as required by Florida law — that was because service people do not pay postage (that law has since been superseded by a federal law). So, yes, military ballots *can* be identified.
Military ballots should be postmarked regardless of whether postage is paid.