Yes the overriding of Affiliate tracking links is a little shady, but let's not pretend these youtubers weren't paid a fee to advertise the extension.
Besides, if you want to support a YouTuber specifically then add the item to your basket. Run Honey to get the code and then reclick the affiliate link and the chances are the last click attribution will go back to your favourite YouTuber AND you'll have benefited from any honey codes.
What IS shady however, is the apparent ability for retailers to pay Honey to show certain codes and hide others.