The military did not use turbo-charged 250s to my knowledge. The NHC250s were all naturally aspirated, at least those in the trucks I have ever seen (M809, M939). The NHC250 puts out about 10 more HP, but the torque is about the same between the motors. Still, I think the NHC250 has more power from a dead stop. The 6CTA (turbo motor) has some desirable characteristics, too. It is whisper quiet, for one. Some like that (me), some don't (those who want beefier sounding motors). My recommendation would be to compare the condition of the trucks, how the motors run, and the prices. If all things are equal, I'd take the A2 (with the 6CTA motor). However, if the NHC-powered truck was cleaner/much cheaper, that would probably be my choice.
As far as I have been able to tell, all of the original motors were black. With regard to the 6CTAs, they switched to tan motors in 91 or so (a tan 6CTA does NOT indicate that it was rebuilt, again from my sample of half a dozen or so, but more that I've seen...this does not mean that someone could not have a rebuilt tan motor). The tan NHC250s are either new crate motors or rebuilt, although most of the rebuilt NHC250s I've seen have been green or black. I am sure others have observed other things.