I certainly hope that Shi never joined them and also took control over the spawning ground AKA Mariposa Military Factory.
Damn NCR and their crap expansion.
Their no match to the Shi I tellz ya!
I don't think the Shi would have joined the NCR. Their technology is just as advance (if not more) then the Brotherhood. Remember, they have so much spare advance technology that they are afford to sell power armor and energy weapons to outsiders. And if you read the notes on their scientific research, you will see that they have in the process of developing things like a new energy source, aircraft, and even space flight. Unlike other settlements in the wasteland, they really don't have a reason to join the NCR.
But perhaps the two powers can form a alliance or at lease sign a treaty of friendship. In Fallout 2, both powers only had limited contact with each other and their goals doesn't seem to be in conflict.