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EU countries have real ID with biometrics though...

I believe biometrics were required only recently.

It's been a requirement longer than the three years this woman has been officually dead. Of course, perhaps she didn't have a passport before

From the article, she found out she was dead when she tried to get a passport.

Yes. EU passports are valid for 5 years AFAIK. The article doesn't say whether she previously held a passport or not.