Someone once said, "Wish in one hand and crap in the other and see which one fills up first". You would be better off trying to change the graphics in Dangerous Waters than to mod this game into a modern nuclear powered one with missile systems and wire guided torps. I think it would actually be easier and way quicker to hack the Dangerous Waters game since it only has 2 items that need changing - graphics and dynamic campaign. SHIII would need about 50 to 100 things changed minimum to make it a modern day simulator and that would take A) forever and B) cost a fortune to create.
My suggestion is to learn to like what you got! I mean, nobody ever tried to change the original Super Mario Bros. game into Sonic the Hedgehog back in the day. We used to buy a game and love it for what it was! Geez
What's happening to kids these days?