I hope this question isn't too broad or vague, but I'm interested more in the ideological arguments implicit in the novel than whether or not this or that period detail is "accurate," though those questions are certainly related.
This is a novel by an Australian author that attempts to represent the perspectives of both early modern europeans and early modern japanese people.
The depiction of "the east" by scholars and artists of "the west" is, I know, a subject of great interest to many sorts of scholars, and I wonder if they come to any sort of consensus about the nature of that depiction in this work.
The eminent historian of Japan Henry D. Smith II, who taught for years at Columbia University, published an entire book about the utility of using Shogun to teach Japanese history. The multi author edited book, Learning from Shogun: Japanese History and Western Fantasy (1980) drills down into the many details that the book gets correct, and also of course the many places where historical inaccuracies get in the way. A postscript explains that the TV miniseries excised many of the best parts of the book and resulted in a far more anachronistic, romanticized product. The authors of the chapters include many noted scholars of Japan, including David Plath, Ronald Toby, William LaFleur, and Susan Matisoff. Smith himself contributed 5 of the 12 chapters. He has made the whole book available as a free PDF on his website: http://www.columbia.edu/~hds2/learning/Learning_from_shogun_txt.pdf