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You will need to show visa documentation to board the flight to Canada. Assuming the rest of your family is traveling on your Pakistani passports and if your Iqama status is noted in those passports, the airline may wish to see his Pakistani passport as well at check-in to make sure he is documented to leave. But they should accept his US passport as proof of permission to enter Canada.
The question would be if Saudi Arabia requires proof of travel upon your return. This happened to us in Africa, as my daughter used her second passport to avoid visa issues, but then was hassled since her exit visa from the previously visited country was not in the passport she presented to enter the next country.