I think Willya hints you what shelves each book is in, too. When I did that quest, I checked Willya just to make sure, and she said three numbers. So my guess is that she tells you where the books are, but I didn't bother to confirm it.
You may be right about that, but I never talked to her while looking for books. On top of that, the bookshelves are not numbered as far as I know, making those numbers next to meaningless unless you know which bookshelf is which.
As those hints from Willya were not 'necessary' to complete the quest, I never looked further into it. I should probably try and confirm the numbering.
EDIT: You are correct. During the quest for 'Fairy Tails'<sp>, WIllya will indeed give you three random numbers from 1 to 9 that are bookcase references. (This does not happen for Manjula's quest, so you have to manually look at all shelves for her Kamasutra book.)
The 'numbering' system starts in the upper left of the library and travels to the right. The bookcases are grouped in lots of 4.
In the upper left the 4 they are numbered: 1, 2, x, and 3. ('x' denotes a bookcase that does not highlight and is skipped in the counting.)
In the upper right, the numbering is: 4, x, x, 5.
In the middle right, the numbering is: 6, x, 7, x, (Willya).
In the lower right, the numbering is: x, 8, x, 9.
So, if Willya gives you the numbers 3, 5, 8, you would got the the upper left of the library, and look at the last bookcase in the row (3). Then for 5 you would go the the upper right and got to the last bookcase in the row. For 8, would go the lower right and look at the second bookshelf from the left.
I will update the walkthrough with that info.