Ok yeah, that horrible. In Slovenia, your fingerprints (for biometric passports) are sent along with the print order to the manufacturing facility and then deleted. For all photo IDs (passport, ID card, driver's license, weapon permit), your photo is either scanned and sent along with the order or uploaded to a database that deletes it after 2 weeks. Nothing is ever stored permanently or accessible by anyone other than the people and systems directly involved in getting your document made. *
* That is, of course, what the law says. I have no reason to believe "the government" is breaking that law, but no way to verify either. It would probably be discovered and leaked very quickly if they were though.