Why do NOS Tubes sound better than new tubes?

Better trained people and better materials back then. As far as one tube sounding better than another, it depends on the application.

They were also allowed to use hazardous materials and work processes that would never be allowed today.

Back then the Military had a great need and relied heavily on ruggedness as well as quality. Can't remember where I read it, but the article stated that they spend much less time creating the vacuum in modern tubes. Back then, an hour on the vacuum pump, now 20 minutes. I never had a nos tube that was dated before 1940's and they were great. If quality was waning then, hard to imagine how good the tubes from the 20's and 30's sounded.

I have absolutely no idea "why", they sound much better, but I can tell you with certainty that they also last a lot longer. That last factor, plus the sonics; justifies the higher price for me.

Because they were made better.