So while thinking back, they make all of these references to various past Fallout locations, and I just realized, they never made any mention of what happened to the Shi. Even vaguely the game mentions most past Fallout 1/2 locations, and yet no San Francisco, that was one of my favorite locations in F2.

Yeah I have been wondering that myself. I hope there is talk of them in a DLC. FO2 says they make their own Empire which is possible because there are no NCR locations close by but NCR would come incontact with them at some point. Due to the Shi being so damn advanced and most if not all know martial arts I doubt NCR would commit to a war against them. Did they form an alliance? The Shi are peaceful. I too would like to know about them. NCR took Navarro which is North of the Shi.