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It's less that one HN user could get a kickback, and more that if posting your own affiliate links was accepted practice, HN would end up being flooded with such links any time they were remotely tangentially on-topic.

If they were shady about it, perhaps. I have no objection to affiliate links that are disclosed.

Can you generate an affiliate link where the affiliate fee is directed to a non-profit?

If the non-profit has a known affiliate code, adding it to any random Amazon item should be sufficient.

There is also AmazonSmile, although I am not 100% sure whether affiliate links still generate revenue when using a Smile link.

Smile transfers a portion (0.5%) of the sale to a charity of the buyers choice. You can't force or even suggest one in the link and it only applies to smile.amazon.com links. I think St Jude's is the default though so they may come out ahead if you change the URL.

I have enough of a problem with the link essentially advertising Amazon, to be honest.