Because the judges on the High Court have changed since the last time a similar case was heard.
20 odd years ago, the High Court upheld the constitutional validity of indefinite immigration detention in the case of Al-Kateb v Godwin.
Similar cases brought since that time haven't gone to fruition so the recent case of NZYQ v Minister of Government was the next time a determination was made and the previous ruling reversed. Maybe if they'd got him out of the country or detention before the case was finalised everyone would still be locked up. IIRC they tried to get the USA to accept him but no dice.
