You are right, in Japan it is not considered smuggling because they are from Japanese waters. However, there may be local laws in Japan limiting or restricting their removal from the ocean. It is considered smuggling if a CITES protected species crosses boarders with any of these countries:
http://www.cites.org/eng/disc/parties/alphabet.php
Remember, it was not Japan that put it on the list so only they can gain from the species, but an international oversite committee.
If the Japanese were reproducing them and selling an aquaculture species then they wouldn't have to "smuggle" them and they would be exported with proper CITES permits. Since there have been 0 CITES permits filed for
Rhizotrochus typusin the US, you can safely assume they are all illegally here.
(plus if there was successful aquaculture of
Rhizotrochus typus this would be big news in the reefing community and we would all be aware of it - it's not like some secret Japanese facility underground where they are growing corals).