The only places I believe you'll get a 2000 bill are at banks or currency exchange offices. 2000 yen bills are never given out as change! (though I see no reason why they shouldn't)

As an experiment I checked out the 5 vending machines in my office. Two are standard drink machines, two are coffee machines, and one is a snack machine. None of them take 2000 notes. There are some machines in Japan which do take 2000 yen notes but I wouldn't count on it!