Having done a similar project[1], that also includes affiliate links to Amazon and being called a spammer by some people because of that, I really appreciate your stance, that if a project adds value, monetizing it is okay.
Moreover, I'd like to add that affiliate links are less intrusive and dangerous wrt to malicious code and user privacy. I wonder why Adsense et al rarely get called out, but affiliate links do. Maybe it's my confirmation bias or it's because people don't see those other ads, because of using an ad blocker.
I think your hunch is correct — we hover over the links and see it in the query string. There's probably a Chrome extension out there somewhere to strip affiliate links from URLs, but honestly they've never bothered me because they don't detract from my experience.
Moreover, I'd like to add that affiliate links are less intrusive and dangerous wrt to malicious code and user privacy. I wonder why Adsense et al rarely get called out, but affiliate links do. Maybe it's my confirmation bias or it's because people don't see those other ads, because of using an ad blocker.
[1] https://news.ycombinator.com/item?id=10924741