The project has apparently been harassed by some other group I’ve never heard of until today. I still fail to see how that has anything at all to do with HN. The wording of the warning definitely implies they’ve been hurt by HN.
That's because they have been hurt by HN. Not intentionally by HN itself, but they are also not the only target.
As for how you haven't heard of them before, that is a bit surprising. They have been mentioned here plenty of times.
HN being user-driven means they are an amplification and legitimisation vector for anyone who figures out how to abuse it. It's not an easy problem to solve, and I don't think any organisation (commercial, or otherwise) has really found a way to deal with this.
As a human side-effect, most people will either have to have experienced it themselves, or have this as part of their job to understand the issue at all, and will either deny it or assume it's exaggerated. Even those that are on the instigating side will not have a concept of the impact until it inevitably happens to them (as is common in that ecosystem).
That should answer your question: "What’s with the warning on the top?"
Perhaps you expected a list of all sorts of interactions between this website and that website, but I doubt the project volunteers kept a ledger to share that with you and that in itself would incite reverse brigading which solves nothing.