Pure speculation on my part, but for one thing, being part of a large network gives them more data and better ability to screen the quality of the people who apply to the affiliate programs. There are merchants on CJ who will take anyone who applies, and there are others who only want those who have proven they can produce. (The more green bars you have, the more e-mail you'll get from merchants inviting you to join their programs.)
If they were to run the program in-house there's still the cost of resources and hiring the right expertise. I expect both those merchants get massive numbers of applications and have a huge number of active affiliates - not a trivial task to manage!
And who knows - maybe after running the numbers they determined that the networks were the more cost-efficient option.