The affiliate link part is not a scam.
The industry standard model for who gets commission is brought up in the video, it's "last-click attribution" (this does not actually have to be a click but some interaction). This model means that the last interaction/touchpoint gets 100% of the commission no matter how potentially influential earlier interactions/touchpoints were. It's by design that the most recent interaction/touchpoint with a site/brand is going to be credited for the user converting (e.g. buying, subscribing). The video focuses a lot on the URL change and cookies but those technical details aren't important because that's simply the interface and the storage mechanism for how the "last-click" is essentially declared and remembered by the different sites. Honey or not, whoever is the most recent touchpoint is always going to set it up so that your browser ends up telling the site that they were the last touchpoint and in turn indirectly changing the cookie. In a system of whoever puts their flag down last gets the prize, nobody checks if somebody already put their flag down before putting theirs down and we shouldn't expect honey to either. The model has its criticisms and drawbacks but everybody should have known the rules and that another business wasn't going to forfeit their arguably valid claim. The model assumes that the last touchpoint was the more influential but that's not always true. E.g. If you watch an LTT video review that makes you really want the product then later you click a random targeted ad, it will override the LTT attribution.
One thing that bugs people is that Honey will still set themselves as the most recent touchpoint even if they don't actually find you a coupon. Which also doesn't really matter because its still the the last touchpoint with the site/brand that has a potential influence whether it returns a coupon or not. The actually scam part where they can lie about not being able to find you coupons is also used as a way to affirm buyers that they are getting the best deal so that they don't have to worry or go check that there's a way to save money with a code elsewhere.
The only scam part is the part about advertising giving you the best deals and then holding deals back from customers.