This is not actually true, the Emergencies Act does not override the Charter of Rights and Freedoms. Anything that happens under the Emergencies Act may be challenged in a court.
"AND WHEREAS the Governor in Council, in taking such special temporary measures, would be subject to the Canadian Charter of Rights and Freedoms and the Canadian Bill of Rights and must have regard to the International Covenant on Civil and Political Rights, particularly with respect to those fundamental rights that are not to be limited or abridged even in a national emergency;"
https://laws-lois.justice.gc.ca/eng/acts/e-4.5/page-1.html