Horiemon has been rubbing old-school Japan the wrong way by challenging the establishment with clever financing and takeover attempts of the media etc. I can see how he would get targeted. On the other hand Japanese companies like his tend to be sloppy so I wouldn't be surprised if they find something. It would be unfortunate if they end up slapping Livedoor down since I think he was serving an important function in Japanese business and this looks like a typical set-up.
UPDATE: I haven't confirmed this, but I just heard a rumor that the National TV Network (NHK) was reporting the raid before people at Live Door knew they were being raided. ;-)
UPDATE 2: Live Door is Skype's Japan partner.
UPDATE 3: Apparently the first notice Live Door got of the raid was when Network TV called for an interview. TV knew before they did.