There's an interesting cognitive bias where people who are intelligent and informed about one domain, try to interpret information outside that domain. This stereotypically affects doctors or engineers making pronouncements of things as laypersons, and underestimating their own ignorance, commit errors without realizing it. Hacker News is an excellent place to get insight on technology. However, the lack of formal training often means that when other domains are discussed, we get armchair biologists or historians. That is happening here. (The loss of Y-diversity is much, much earlier in date than the Late Bronze Age collapse: starts at roughly 10k years ago, with a little variation depending on what part of the globe you are looking at.)

Here's the original article that caused such a stir in 2015. Figure 2 shows the sudden drop in the reproducing Y-population globally (meaning it cannot be explained by genes or migration).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381518/

The paper cited in the article alters the date of the event, but really there's a lot of uncertainty remaining.

https://www.nature.com/articles/s41467-018-04375-6

The best current hypothesis to explain this drop (and that no similar one occurred for the reproducing X-population) is the conflict between predominantly agricultural societies versus predominantly hunter-gatherer societies. Until sufficient evidence has been found to rule out this or alternatives, take any explanation with a grain of salt.

Look at Figure 2, and you'll notice the Y-axis are different. Between 50-10kya, the effective reproductive population was 3-4 times larger for women than men, globally. This fits with modern anthropological evidence of polygyny in early hunter-gatherer cultures (loose polygyny with on average 3-4 wives per successful male over a lifetime, but with limited ability to enforce fidelity). Y chromosome diversity tends to accumulate, albeit at a lower rate than the X.

An agricultural community is likely to be much more homogenous in terms of Y-chromosomes, than a hunter-gatherer one. Power is much more effectively concentrated in these communities, allowing leaders to amass more wives and enforce fidelity much more strictly than in hunter-gatherer societies. Stories of King Solomon's wives, or Sultan Moulay Ismail of Morocco (who reportedly sired hundreds of children) are an easy way to visualize this.

While man-for-man, a hunter-gatherer may be healthier and stronger, a hunter-gatherer society may find themselves vastly outnumbered by an agricultural community. Over time, hunter-gatherers would find themselves pushed off of prime land onto marginal land. The newer article mentions a founder effect. Where are these Neolithic pioneers coming from and where are they going to? From agricultural communities, expanding into territory previously held by hunter-gatherers. While certainly many deaths occurred due to combat, Y-chromosomal diversity loss also would have occurred to disease and famine. The agricultural population would continue to rise, while the hunter-gatherers would struggle to maintain on more marginal land. History is replete with stories of taking women, so if this scenario is the best explanation, it is unsurprising that there was not a corresponding drop in X-diversity.

This sort of scenario occurred globally. Agriculture independently arose in many places: the near-east, sub-saharan Africa, China, Mexico, the Andes, and possibly others. We've seen what happened to the Americas after Columbus. Similar mechanisms help explain the population-level Y-cide on smaller scales that probably occurred during each of the agricultural expansions above.

This hypothesis, while probably the most widely-accepted at present, is challenged by some of the evidence in the newer paper. It will be interesting to see how it falls out once the original authors have a chance to respond or additional voices join the conversation.