Let me caveat this answer by saying that I've only been learning for a year and use of は is a mind bending subject.
First of all, は does not mean 'be'. If you really think this then you have a serious misunderstanding. In your example the function of 'be' is provided by です. は is the topic or contrast marker. For me the distinction between topic and contrast can be quite blurry, but in these sentences I'd say it's contrast.
Western books are sold in that shop
I don't know about other shops, but at least in that particular shop, western books are sold.
That's obviously an exaggeration, but hopefully you get the idea.
From the topic marker point of view, I'm sure you would be happy with the following sentence:
That shop is Momoko's shop.
You've introduced a new topic, 'that shop', to the conversation. But what if you wanted to talk about what happens in the shop? You need to put で on the end, but you're introducing a new topic at the same time so you need a は. No problem, just put the two together and you get your original example:
Which of the two interpretations is more appropriate would be determined by context.