Typhoon 13 (I really wish the world would take on this simple Japanese way of naming typhoons) is right now south of Tokyo, but the wind and rain is already hitting the Tokyo and Narita area. It looks like Narita will get the full strength of the typhoon in the AM of the 9th. So I would expect quite big disruptions to traffic departing and arriving during the 9th.
JAL should be quite used to dealing with this, but it has been reported that a lot of the information comes in Japanese only.
My two points of advice is 'don't panic' and Google your alternative connection options if there are cancellations. It is always easier to discuss if you know some options in advance.