Yes, Vasily, you're right. But...
1. I may refer someone to Subrion not only by link, but also by any other way. For example, I am talking with someone by IM and say him. Buy Subrion, link:
http://www.subrion.com. He reviews your site 2-3 days and after that he decides to buy a license. Actually his cookies may be deleted in this period, but he may know that he referred by me and may insert my affiliate ID.
2. I may want not to have an affiliate link. I may want to have a direct link to your site and allow visitors to add or not add my affiliate ID, cause that is not so comfortable for anyone when he is referred to site via affiliate link. That's a common trend in all affiliate programs.
3. I may want to have a special programm to sell Subrion. For example, I may say: If you will be Subrion and add to it this affiliate ID, I will give you any good or anything else. I think that's good for Subrion and for me as well.
Cookie based affiliate system doesn't allow to work more dynamically. This system will allow affiliates to be more the partners of Subrion instead of just link affiliates of it
P.S. Btw more affiliate programs go by this way, e.g. the last is vBSEO that just added
Referred By optional line to it's order form