How did Bane know the exact location of the Batmobile in the Dark Knight Rises, since Lucious said it was off the books?
It is not that hard, once you know who the Batman is. The whole R&D department was off the books then, but it was not always so.
Also, he might have just looked into people close to Bruce. It's only 2 people (Alfred and Lucius, since Rachel died), and Alfred is not a very likely candidate for the Batman's armory-man.
Miranda/Talia is on the Wane Enterprises' board of directors, so she ought to have an easy access to all the files, present and past. Knowing what to look for, and that Lucius must be on top of it,
I really see no problem in finding out that there used to be some huge "Applied science" division that "disappeared overnight". It was said so in the second movie, also found out about from the books, by a person with no knowledge about the Batman. Note that scene also includes sketches of Batmobile, formally known as the Tumbler (or by some "long, dull W.E. code"), that Reese managed to find in the archives. Miranda/Talia has far more knowledge, resources, and motivation than Reese.