Why is it in these invented HN scenarios that the engineers just happen to have absolutely no agency?

Because I've personally seen it. Engineer says this is silly, it will blow up in the long run - told to implement it anyways. Not much to lose for the engineer to simply do it. Substitute engineer for any line level employee in any industry and it works just as well.

I've also run into these local maxima stupidities dozens or more time in my career where it was obvious someone was gaming a performance metric at the expense of the bigger picture - which required escalation to someone who could see said bigger picture to get fixed. Happens all the time as a customer where some sales rep or sales manager wants to game short-term numbers at the expense of long-term relationships. Smaller companies you can usually get it fixed pretty quickly, larger companies tend to do more doubling down.

It usually starts with generally well-intentioned goal setting but devolves into someone optimizing a number on a spreadsheet without care (or perhaps knowledge) of the damage it can cause.

Hell, for the most extreme example look at Dieselgate. Those things don't start from some evil henchman at the top saying "lets cheat and game the metrics" - it often starts with someone setting impossible to achieve goals unknowingly in service of "setting the bar high for the organization", and by the time the backpressure filters up through the org it's oftentimes too late to fix the damage.

Because: who would refuse more money?

I don't think this evil boss and downtrodden engineer situation can explain what we're seeing.

Your theoretical engineers would figure out pretty quickly that crashing a server slows you down and the only way to keep the boss happy is to avoid the DDOS.