I've always heard, that they are very accurate as far as historical events, political/religious factors, etc. go. I have read the Asian saga myself, and they are some of my favorite books, but I'm not much of an Asian historian, so I always wondered how they hold up when somebody who knows the history through and through actually reads them.
Check out the book Musashi by Eiji Yoshiokawa- in the forward it talks about Clavell's novels and how they are not authentic and have a lot of western conceptions towards Japan and Japanese history. For one the love story in Shogun is a typical western romance, whereas in Musashi there is a much more traditionally Japanese depiction. Great book Musashi, guy also wrote a book called Taiko about Nobunaga, Hideyoshi, and Ieyasu Tokugawa.