I want to place their native shopping ad at the end of a few of the pages on the site and maybe one text link inside the content on those same pages.

I do find Amazon works pretty well in terms of conversion. They are really good at converting and cross-selling, but I don't want to risk rankings if Google takes a negative view of Amazon links.

On a different note, I am creating a site that will have a lot of affiliate links. I expect about 50% of the pages to have one or two affiliate links per page and around 20 will have possibly up to 20, which obviously need to have the affiliate links if I am going to generate commission. These won't be Amazon links.

This site will be a mix of content and affiliate. These affiliate links will be for the benefit of the users because they expect to be linked to the product pages. Not including an affiliate code will generate free promotion for those sites.

If the site is high quality, provides a lot of value to users, does it matter if affiliate links are included on a lot of pages?