I'd be careful of doing this. I would not place multiple shelves of books under the rafters, esp. at mid-span of the floor or under floors that heavy things like bookshelves and large appliances like refrigerators or ovens.

I would be careful for 3 reasons:
1) Additional load -- Book storage is quite heavy. One of the heaviest load patterns in structural engineering is for library loads, due to the book storage.
2) Earthquake hazards
3) Creep -- Sustained loads on timber structures slowly make them permanently deform. You don't want to have a bunch of sagging joists and a sagging floor above.

(By the way, I don't think the members that you refer to are rafters. Rafters are used to create a pitch on a roof. I think you are looking at using joists, but no one will care unless you're an engineer or an architect.)

Also, take care in designing the connection. From the picture, it looks like you're nailing or screwing through the bottom of the shelf board into the bottom of the joist. This could wreck your joist if you split it and could help the pull-out of the nails since you've put them in tension. A better connection detail would put the nails or screws in shear, having the nails or screws come into the joints horizontally from the side.