Welcome to the Q&A Forum

Branding and visibility issues aside, from a pure link standpoint those links don't count (or shouldn't per Google).  Google wants affiliate links to be nofollow since they're advertorial (Matt Cutts on the matter - <a>http://www.youtube.com/watch?v=1SmlsfSqmOw</a>).  Cutts also says affiliate links should be disclosed adequately.  Now on the other hand, you're right that these links are benefiting a company that has these relationships set up.  I'm sure they're getting visibility, traffic, and ultimately sales.