Say you have a product, let's say I'm selling shampoo for example and I rely on affiliates to sell my product. So they link to my site with http://theshampoostore.com?&=3434 and use the link name 'shampoo' to make something like this: Shampoo. What symbol could you use that would be recognised by php, but google would ignore what's after it? So therefore missing out the ?&=3434. Or, isn't it important for google? If you have hundreds of different affiliate links back to your site, with varying address', would it not be ideal for SEO?
Is that a question or an assertion? What you want back to any site is "hundreds of links with different addresses". We can talk about the specifics of the particular link, but in general the more links the better and the wider the range of pages and/or sites they are from the better. I can't see any potential harm from affiliate links, with or without the affiliate code.
Sorry, it was meant to be a question - I've edited it to make more sense, although you'd think english isn't my first language at times!