It wasn't projected in 4:3 because most movie theaters can't do it anymore (or so I've been told). Kubrick shot this composed for 4:3. Not to say he didn't pay attention to the widescreen version, but Eyes Wide Shut (and, for the record Full Metal Jacket and The Shining) were all filmed and intended to be scene in 4:3. Widescreening would cut off half the movie.
It has now been confirmed on the basis of his storyboards that he composed for 1.85 (as one would expect) and protected for 4:3.