Can a particular category be hidden from an individual affiliate. Say for instance the affiliate would like not to have "pet food" show up when his link is used??
Absolutely, but it's going to require customization that's specific to your navigation xml package and requirements.
The easiest way would be to hide the category from the menus in the xml package you use for navigation based on the current users affiliate.
However, 'hidden' could mean quite a bit more than that. If you need to hide the products in that category all together (for example from a users search), you'll need to do quite a bit more customization including the GetProducts stored procedure.