That's a fun question. Personally we do not have more than a couple dozen books in total at our house. This is more the product of my generation plus living in Japan where no one can afford the dead space for a book shelf.
For the subject matter I would say your best set of resources is GDC presentations. Our industry's great minds never write books, or even web articles for that matter. Best they give are the occasional GDC presentation. Even then Miyamoto has maybe given a couple hours of publicly accessible teaching material in his entire career.
If you are interested in Rendering that fields has a good number of useful books written. Design itself is more about "theories of games". Everyone has their own theories, mine might be more influenced by Sid Meier than anything.
My experience has been with a couple western designers, but more so stalwart japanese designers. On the Japanese side you'd be surprise how "personal" the design philosophies are. Westerners tend to be more rule driven, and thus if you want a systems driven understanding of design that needs to come from the west.
The training system in Japan is more apprenticeship driven. What the west would call designers first start as planners. Planner being a rather low level job with lots of manual grunt work. Then within a company the senior designers will couch the juniors on the subject of game design.
Thus there indeed does exist tomes on Nintendo's game design: but no one outside Nintendo has ever seen it and no one Ex-Nintendo can talk about it. Just look at how Ojiro (https://twitter.com/moppin_) designer of Downwell went silent after joining Nintendo, then after leaving has remained silent.
Off the top of my head I know for sure Nintendo & Bandai use this "in-company learning" structure. Square Enix being a collection of fiefdoms tends more towards hiring a designer they like then putting them in charge of a team. Hence how you got Tokyo RPG Factory.
Note I'm approaching this with the understanding that a good game only has 1 lead designer. In Japan this is the game's director. It might be that in the west game's have a more group driven approach.
