Oh ok, that "Program" folder is just the folder inside the Start-menu where the shortcuts are placed. Or whatever Windows 8 makes of it these days. That has no issue with installing the game and modding attempts not succeeding. Choose wherever you want it to be, and still be able to find it later.
The important thing to watch out for is that the game is not going to end up on the harddisk in
c:\Program Files (with or without x86)\whatever_is_inbetween\SilentHunterIIIorWhatev erItIsNamed
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