I'm almost always a fan of the theatrical version of films when it comes to additional content. In a perfect world, the "uncut" scenes of gore, nudity, coarse language and violence are included in a cut of the film, but the original theatrical experience is preserved. I am really not a fan of a director revisiting an old work (Alien, Star Wars, etc. are all worse with the changes), I think once a film is made it becomes property of the viewers and the people who pay to see it. Imagine if Da Vinci, all old and senile, decided he wanted to paint a fedora on his Mona Lisa. Yeah
In the case of Close Encounters, it also just so happens that I prefer the theatrical content, too. As others have said, the ambiguity in this case is the best part.