Didn't watch the video, but if replacing a referral code is wire fraud for depriving a content creator of money, then deleting a code is also fraud, which seems to imply that I, as an individual, can't edit out a referral code from a URL I receive. I think referral codes are a sales device and there's no guarantee that just because one sales person put in the effort of convincing a person to buy, it's still allowed for that person to buy from someone offering a cheaper price (which is what I gather Honey did by finding coupons).
Discussion
They still replace the referral code even when there's no coupon found, it's actually unrelated. They go through hoops to trick you into clicking useless modals right before checkout, and snag the referral reward using these clicks. This is what made people angry and uninstall the plugin.
The script they gave youtubers to read is also a bit of a lie, they don't apply the best coupon they're aware of if the merchant has paid what is essentially a ransom to forbid Honey to apply these coupons the merchant would like to keep more exclusive.
First paragraph doesn't sound like fraud to me. Second paragraph does sound like false advertising.
I'm think it's mainly fraud against the merchant, because Honey faked being the referrer.