All VCA stores in Japan offer duty free for those who can provide a foreign passport/for non-Japanese nationals and residents. The different prices are already on the price tags. It’s not one specific store/location so don’t worry about that. Moreover, they will do it for you in the store, hassle free, when you make your purchase. It’s a very easy process.
I would say there is no easy answer to your second question. No one here will be able to guess how stock will be at that time when you’re traveling to Japan. Over the past couple months, stock has been low. Could that change at any time? Sure it can. Is it guaranteed? No. Will you be majorly disappointed/ will it ruin your trip if you can’t get the piece you want? If so, I wouldn’t go through the hassle. I would just purchase it here and now if your heart is set on it. However, if you’re going there with an open mind and the kind of attitude “if I find something great, if not, it’s no big deal” then that’s a different story. It really just depends on you and your expectations going into it. We also can’t predict how the Yen will be compared to the USD. The Yen was very weak when I was there this fall.
I know when I purchased my GMOP vintage Alhambra pendant in Ginza Six in October they had low stock. She did,
however, show me two pendants and I picked one. I actually just went to the store without an appointment to see what would happen with no expectations and it happened to work out.
Shortly after I left Japan, there was a price increase for both VCA and Cartier to even out worldwide prices because with the weak Yen it made my vintage Alhambra pendant to be about 2,250 USD in Japan as opposed to 2,900 USD plus an additional 7% sales tax in the states (3100 USD.) As you can see, they were trying to even that out because it’s a big difference but I jumped on the opportunity when offered the piece.
Best of luck! I hope you find what you’re looking for xx