The whole point of affiliate links is that they're generating sales that wouldn't have existed without- it is essentially an incentive for people to advertise for Amazon in organic ways. Whether the money goes to the affiliate or the smile program at that point wouldn't really make much difference, and actively undermining the people who post affiliate links seems like it would be a stereotypically idiotic corporate split brain thing to do.

I don't often click on affiliate links, but I also don't recall seeing the smile reminder when I have used them. YMMV I guess.