They actually shot it as PG-13 film!
I find this a very strange reason, even DTV sequels for PG-13 films usually are R rated, and I find it very strange that the marketing department wanted a PG-13 for a lower budget action film that will never reach an big audience. But at least it got an R rating.
In this interview the fight choreographer talks about how he didn't know about until two weeks before filming, and that he had a planned some really violent and bloody gags:
http://www.outlawvern.com/2013/09/25/interview-with-tim-man-stunt-chor eographer-on-ninja-2-by-david-j-moore/#more-19749
It seems like they perhaps filled the film with CGI blood ala The Expendables film. The film still looks very good, and the reviews are positive, but I'm still disappointed the Isaac Florentine and Scott Adkins agreed to this, I guess they where desperate for the film to be made.