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Even if it is taken up by soul silver, it's a a gen 4 game ergo not going to be talked out nearly as much as these games will be, and often talked about in conjunction with heart gold (ergo, HGSS). For the rare case people want to refer to soul silver alone as SS, there's context too. Ergo, SS will prevail is my bet.
Probably S&S. I was never a fan of using multiple letters for one-named games like sumo and now sushi (neither of which feature Japan-based regions!). S&S is less letters without being straight up SS. If I were to just use SS I'd get a nagging in the back of my head each time.
Like others, probably SwSh since it's similar to "Swish" and easier for me to remember. I've been hearing the other initials have bad implications as EC had said, so yeahhh.