Wow, that really does suck.
The process will formally commence in April and will primarily target users of Winny, the most popular file sharing network in Japan.
However, I doubt that will stop Torrent users since Torrents can be used in LEGAL means. It also won't stop the old fashioned FTP methods and probably people will go back to the old fashioned warez method of hunting open servers to use their FTPs.
What I expect to see if that Japanese file sharers will located servers outside of Japan to place their files at and then go back to using torrents outside of Japan. I can also see that they will use more sites like Megaupload or Sharespace to upload unless Japan blocks those services as well.