I thought it was, ironically, "An Alan Smithee Film" that ended Alan Smithee's "career"? Although the IMDB link shows credits after "An Alan Smithee Film".
American History X is still credited to Tony Kaye, although IIRC towards the end of the editing process it was taken away from him and again IIRC Ed Norton finished it? Apparently this probably was the first "good" film where the director requested a "Smithee" credit (but the DGA didn't give it to him).
Have a look at Wikipedia's listing, which is quite informative:-
http://en.wikipedia.org/wiki/Alan_Smithee
In short, Smithee was dropped after "An Alan Smithee Film", but has still been used since, and nowadays a pseudonym is used on a case by case basis, the first such being "Thomas Lee".