When I was last at Junkudo, I spotted this terrific book, THE SECRET SENSE OF JAPANESE MAGAZINE DESIGN. It was put together by CAP — the company behind most of the great layouts you see in Japanese magazines these days — and covers the history of Japanese magazine design by spotlighting 12 or so magazines (titles like POPEYE, ESQUIRE, and STUDIO VOICE). The intro is bilingual, and the rest of the text is Japanese-only, but don’t let this stop you from picking it up, since it’s all about the layouts found within, and that’s what you mostly get here.
Also, while looking up the link for CAP, I was greeted by a major update to their website. Should now give you a better idea of what they’ve done in the past.