You are definitely entitled to a refund under APPR regulations if as you describe, the CX flight was delayed from 0150 to 2230 the following day (more than 9 hours). It should not matter that you took the YOW/YYZ segment (presumably this is all on one ticket). Your TA should know this, especially if they are Canadian.

I would write in (or have your TA contact) Customer Relations or their Agency Sales contact stating the above, demanding a full refund, and C$400 per person cash compensation that you are entitled to, failing which, you can complain to the CTA.

Also, I know this doesn't matter now, but there are many, many options from YYZ to TYO. Hindsight is 20/20, but I'm almost certain there were other flight options to get you to Tokyo on time. I certainly would not have abandoned the cruise. Something doesn't add up here.