One of Tokyo's cooler concept hostels has beds tucked inside bookshelves (most books are in Japanese, but some are in English). 'Compact' bunks have 80cm-wide beds; standard ones (from ¥5185) have 120cm-wide beds and lockers. Note that the 'bookshelf' room is also the common area (though bunks have curtains); the 'bunk' room has more privacy. Payment by credit card only.
The hostel opens up its lounge for day time use between 1 and 5pm (¥540 per hour or ¥1500 for the whole time).