There are no affiliate links on confirm pages because you cannot pass custom variables to a confirmation page. The thank you page drops all relevant cookies before you reach it though, so you get credits on all sales.

This is working as intended and the same way we have always done it. Rest assured, you will be credited for any sales made through the opt ins before they reach the Thank You page. Just make sure you have entered your JVZoo, Clickbank, W+ affiliate IDs in your Profile.