There is no reason that affiliate links would need to be nofollow since the links do not normally go directly to a merchant's site. Some affiliates always nofollow their links and others never do, but since the links travel to a network where they get redirected and are not links to a merchant directly it is not normally a negative.
A relatively small number of merchants do use some proprietary in-house system that goes directly to their sites, but google knows what affiliate links are and since Amazon's in-house system doesn't seem to have hurt them I would consider nofollows to be a non-issue. It is not viewed as a link scheme or paid links.
I would be much more concerned about keeping up to date with the FTC regulations that make a merchant responsible for the claims your affiliates publish in regards to your products. It's one reason most informed merchants prefer to work via networks. A lot depends on your brand, your product line, and how professionally your program is managed. It is not a part time job for an existing employee who has no experience dealing with affiliates.