Whether the fallacy argument applies or not depends 100% on it trying to satisfy both the means and the ends.
"If I flap my arms, world peace will be achieved."
If I flap my arms, and my intent is to achieve world piece, I'm operating under the "arm-flapping" fallacy.
If I'm flapping my arms simply because doing so makes me happy, the "arm-flapping" fallacy does not apply. Yes, it is still true that flapping your arms will not bring about world peace, but who's the moron talking about world peace? Not me; I'm flapping my arms because it's entertaining.
The same thing applies to the broken window fallacy. It should only be invoked if the stated intent is to create net positive economic value through increased economic output. Last I checked, the people prosecuting this war in EVE weren't concerned about net positive economic value. That is true even if they were concerned about a personal economic net positive, which would be assumed to be at the expense of an economic net negative to be borne by the loser of the war. That last part (the recognition that a micro net positive relies on a macro net negative as a result of the destruction) is what separates the fallacy from the truth.
And, as with real life wars, others can have an economic benefit. Particularly those who hold large resource reserves, The price of which will skyrocket as these giant alliances work to rebuild their now-decimated fleets. Basic wartime economics.