While great from the perspective of storytelling, it's little wonder that few games have ever taken up the military applications of nanotechnology. Better to pretend nanotech doesn't exist than to allow it free rein. This is what most games do. If they do deal with it, they do so in an innocuous way. Nanites have appeared on Star Trek in several forms, but do not appear to have altered the nature of Federation life very much.
Technology is just a way to dress up the new fairy tales that Lucas has chosen to tell.
The fact of the matter is that, even if I included an exhaustive list of SF RPGs, you would see the same pattern over and over again. That's why so many SF futures look like 20th century North America with laser guns and aliens. To deal with the effects of a technology like assemblers would alter that equation in ways that few people are prepared to deal with, especially in roleplaying games. Everyone wants merchants and hovertanks slugging it out in pitched battles. Magical matter compilers that can create whole starships in minutes or nano-seeds that can grow houses are really neat ideas and worthy additions to the worlds of roleplaying.