"Please close the window above the bookshelf."
The answer should be 本だなの上のまど"を"しめてください.
The reason is that "を" is the direct object particle and specifically joins the two phrases as a complete sentence.
Using "wa" would still get your point across contextually, but the particle choice is just awkward. "Wo" is much more effective in this case.
Would I be right in saying that it could technically also mean "the window on top of the bookshelf"? And if so, would I be correct in saying that Japanese does not have separate linguistic concepts for "on top of" and "above"? (I.e. the same phrase for both English meanings)
My understanding from these comments is that if you specify in the sentence that what you are talking about "The window above the bookshelf", you would use は to specify you are talking about that area above the bookshelf, and ask to close "it", it being the window.
If you wanted the sentence to be "Above the bookshelf, can you close the window please?" it would be better to say 本棚の上に 窓を閉めて ください. My understanding is this variation splits the area and the object so using に and を makes sense.
I Imagine you would use this second variation if you like to pause in sentences more or don't know exactly all of what you're going to say as you are saying it.