I can only agree with what Logan said here.

I would say, that not all directories are a waste though. If you happen to find a directory with good authority, is still being maintained and is relevant to your niche or location, then I would say go for it. Just always think whether it's worth it or not to go for it. If you're in doubt, then that's probably a sign you shouldn't waste time on it.

Google do not use it in a page's ranking (see here: https://www.youtube.com/watch?v=CgBw9tbAQhU). And since the referral spam is never actually on your site, but only activating your tracking code it shouldn't hurt you.

Besides, I don't think I've seen a site out there who hasn't been hit by referral spam. Some haven't been hit as hard, but still have seen it to some degree. Just set up some filters & segments so you can analyse on the real data. I found it very helpful to read this and this.

Without knowing all the details of the case, maybe it has something to do with searcher intent? Seeing as it's only websites who don't sell the product, maybe that's exactly what the searchers are looking for?

If people who search it are clicking and spending a long time on the top results that are full of info, then it might signal to Google that they found a good result and more of that kind (information pages) will come up higher.

Again, I don't know if this is the case, but it might be a possible explanation for it.

I would start out by making sure you put back the analytics tracking code, since that's not there right now (checked both with Google Tag Assistant & in the source code). So it makes sense you can't see any traffic from search, since there is no tracking. That probably explains a lot of it.