[Nyororin]

Try looking into a Japanese style room. In most western style hotels in Japan, the beds are really very very small and there is often barely enough room for double occupancy - let alone 4 people requiring sleeping space.
Japanese style hotels/inns, on the other hand, are usually a lot more flexible. The rooms are larger open spaces, and you can add further occupants by increasing the number of futons.

If you`re having this problem with expensive, top of the line hotels, then I am going to be as stumped as you - but in general when families travel in Japan they use Japanese style rooms. I mean, I`ve traveled with my husband, son, and his parents, grandmother, and sister - A total of 7 people (6 adults) and never encountered a problem finding a single room for us.