Words count for very little as far as storage space is concerned, but you WILL run into trouble with performance if you end up putting all 1.3 million words into a single Flowchart or a single scene :) As long as you cleverly splice up your scenes and your flowcharts, you can make an infinitely long game, nothing to worry about there.
A quick back of the envelope calculation puts 1.3 million words at around 80mb of data. That's assuming it's all stored in a single text file with no markup. At the limit I guess you probably could put all that into a single Fungus flowchart and scene and just about be able to run the game on a PC - maybe. As wolfrug says you'd be much better off breaking it down into lots of smaller scenes which will help keep the performance and memory usage more manageable.
Thanks for your opinion. For such a big game, I have to create some chapters. Maybe, these chapters represents scenes. So I should go fine. ;)