The overall affiliate channel has become increasingly challenging to manage profitably from a merchant perspective. But it’s very easy for a “manager” to see all of the sales affiliates “drive” and assume that it’s making them money.
If you let affiliate sell for you, you had better invest in a professional affiliate manager that you can trust. If you source it to an intern you’ll lose a ton of money to leeches and fraud.
I usually try to build flows now that don’t ask for coupon codes at checkout (because that leads to deal searching right at the last moment). I prefer dedicated URLs with embedded offers as much as possible.
If you need to go the coupon code route, I recommend how Namecheap does it: they registered a unique domain (namecheapcoupons.com) that publicly list all coupon codes. They rank #1 in organic search results.
But, as a general rule, I encourage you to avoid working with deal sites and coupon affiliates. This is a general rule, but they tend to drive very little incremental revenue. You should also disallow any PPC campaigns using your branded terms.
It should be noted that cookie stuffing is a term for a specific process where a site will inject cookies for thousands of sites with their own referral code on pageload of a landing site they control. It is highly illegal and people have served jail time for it, as it is considered fraud.
What coupon sites do is they tend to hide codes behind a button that onclick will load the retailer's site with their affiliate code, then show the code.
There's a lot of forms of cookie stuffing that are legal, or at least grey, and still seem to me like cookie stuffing, even though they aren't standard, clear-cut, illegal cookie stuffing fraud.
It certainly sucks for the blogs and websites trying to fund their content with affiliate links though. Someone like Wirecutter can spend time and money on reviewing items and then can lose out on the referral commission in the end.
Affiliate comes out of retailer marketing budgets. They set the rates thinking they're paying for certain types of customers from certain participants. Honey is getting paid what the retailers think it's worth - they're skeptical, but it seems to be driving incremental conversion for especially price-sensitive shoppers.
I'm pretty sure that big players do complain and they'll get a "first cookie" or at least partial attribution for the sales they make.