If we can dual-map, perhaps better to map both since they both appear to otherwise be unused. But if not, then... I dunno. Ctrl-S is more standard across other software, but Shift-S has been Simutrans's standard for so long. heh. I dunno which is better.
In most applications, shift is not used, by itself, as a modifier for keyboard accelerators involving letter or symbol keys. Games and graphical applications are an exception, though. However, I have no recollection of hotkeys for saving in any game.
Another thing about shift, is that it is often used to alter, often inverse, the meaning of another accelerator. I don't think Simutrans uses it that way at all.