Except honey does not clarify that it replaces the referral link anywhere. The vast majority of shopping sessions do not have attribution, so adding attribution to them would just drive prices higher for regular users, damaging both users and the sellers.
It could lead to lower prices if they are indeed replacing referrals. Supposing the retailers notice that this is a huge affiliate, basically understand what's happening, and negotiate a smaller commission for these programs (they obviously have a lot of negotiating power since they aren't really getting referrals and could just ban these programs, destroying them), they might have a lower overall cost.
I imagine people running affiliate programs have heard of rakuten, for example, so I suppose they have some reason they haven't banned it (i.e. it actually benefits them/lowers overall costs).
This cost would lead that less creators would participate in the referral program. Because the only criteria to participate is how much money they get from it. Though, maybe a good thing, I am tired with all the tech reviews glorifying new stuff, like it is an ad all the way. The good sign if reviewer has a ref link is that the review is probably optimized to be the last place you visit before making a purchase.