Instead of low noises I was greeted by what I can best describe as a very faint sound similar to what a cell phone vibrating on a hard table would sound like.
Before assuming that the noise was because the speakers are bad, did you rule out vibrations? Are the speakers sitting on a wooden desk or loosely screwed to the wall? Try tightening the mounting screws or placing them on a rubber/fabric mat.
When raised to sufficient amplitude it produced an inaudible but extremely annoying and headache-inducing sensation. When raised further it just played a kind of low tone.
The strange behavior of high-frequency noises is actually normal. As you increase the pitch, you get inconsistent results (including sudden and counterintuitively low notes), especially with cheaper speakers.
Is playing demanding audio through crummy speakers detrimental to their lifespan?
Well yes, playing certain frequencies and amplitudes on speakers that cannot support them can indeed damage them.
If so, can it be abused to create malicious 'speaker-destroyer' files and is this a valid concern?
As to a malicious audio file, it could be made to damage speakers, but what if your volume was low? Nothing would happen. It’s like if somebody poisons a drink. If you don’t drink enough, the poison won’t kill you. If you habitually crank the system and wave volumes to 100% and increase the player pre-amp, then you’ll probably end up damaging your speakers anyway.
I guess this could also be a software issue but I was able to reproduce it on multiple laptops
It could also be the audio-card. Try increasing the PCI Latency Timer option in the BIOS a bit to see if the sound card still makes strange noises.