Actually, Section 1 of the Canadian Charter of Rights and Freedoms sets both the extent of those rights and freedoms and the limits that can be put on them by governments. It is not only the "notwithstanding" clause that can limit such rights and freedom, any law that meets Section 1 limits can also do so. While the courts do claim to look at those limits in their decisions, there is actually very little case law arising from cases where the government would have attempted to provide evidence of the elements of that limit, which are that the limits are "demonstrably justified" and are so in "free and democratic societies".
The Section reads as follows, for anyone interested (my underlining):
1. The
Canadian Charter of Rights and Freedoms guarantees the rights and freedoms set out in it
subject only to such reasonable limits prescribed by law
as can be demonstrably justified in a free and democratic society.
In most cases, the courts simply state and come to the conclusion that limits exceed that last bit and basically set themselves up as sole experts on what constitutes a free and democratic society, but I have yet to hear of a case where the government attempted to use limits found in the laws of other countries that could be considered free and democratic by asking the courts to actually look at those countries and determine, factually, that they are free and democratic.
I think that would be a nice trick. After all, what constitutes a "democratic" society when you live in a country - Canada - that does not elect nor has ever elected it's government, but where that government is appointed at the sole discretion of the Monarch - tradition aside. I can think of so many countries where the head of state and the governments are actually elected by the people.
The matter went beyond Charter violations though, as the judge ruled the invocation was "ultra vires", or outside of the law. To be lawful, the government likely would have needed to amend the Emergencies Act.
And that is the crux here, isn't it. The Emergencies Act requires the proof that the emergency at issue meet the definition set out in the relevant section of the CSIS Act. Even the head of CSIS at the time told them that it did not, and he wasn't the only professional head of department who expressed that position to the government at the time. Unlike the political commission that was struck to look into it and came down on the side of the government - all the while also recommending that the CSIS definition be removed - the courts have no choice but to look at the actual Act as drafted by Parliament and at the factual evidence provided in support of either parties at trial.