Yes and no. The first NOTAM made no mention of humanitarian flights. Normally, those flights are allowed entry, in compliance with ICAO procedures.
As you pointed out, the NOTAM has since been clarified, and NAV CANADA was given authority to deny clearance to humanitarian, medevac and search and rescue flights, unless instructed otherwise by the government. Normally, NAV CANADA takes the pilot's word when they declare the purpose of the flight as humanitarian or search and rescue. NAV CANADA does not verify whether the declaration is true because it does not have that capacity. That's what happened at that time.