I don't see how the seats are easier to obtain from the website. If you asked your agent to make a reservation for Y/B classes, wouldn't it be just as easy, because they come from the same inventory pool?
In terms of the price, I DO agree some simple roundtrip fares quoted are competitive. For example, I just checked the roundtrip of HKG-YVR flight departing on Dec 14th, and the price I got was HK$9080 for restricted ticket. This is in fact very close (if not lower) to the prices I get from my agent when I book in B class travel. (I don't remember exact figures, sorry!)
But the competitive pricing is hard to obtain from the website if you want to fly on routes where only the travel agents have the special offer agreement with the CX. For example, below is what I go from website for the low season roundtrip travel from Canada to Australia:
Economy Restricted Class 5,266.02 CAD
I flew on the same route for as little as CAD$1750 (including applicable taxes in Vancouver).
Finally, regarding the agents. I also use a big agents for all my leisure travel, and the prices I get might not be as cheap as those smaller agents which I don't trust (those ones you see on local newspaper advertisement). I also do not find it worthwhile to make several phone calls to ask for the fine prints for the benefit of few houndreds of dollars. I continue to be loyal to my agent because they provide excellent service to repeated customer like myself, and I find this to be my major incentive to purhcase tickets from the agents.
By the way, I'm not worried about the security issues, because I have done numerous internet transaction in the past.