Here's a couple of updates for Prague in case someone uses the search function and stumbles across this thread. Most of the other threads about Prague didn't contain any helpful info.

Prague, Czech Republic
Dokonaly Trik & Magic Store
(Magicstore.cz)

As of April 2022, this brick & mortar magic shop is currently open. Easily accessible with public transportation, the unassuming shop is a proper magic shop that may be worth your visit. Although the product selections weren't as extensive as many shops throughout Europe and the United States, the manager of the shop was very knowledgeable, friendly, and spoke excellent English. The shop had a wide selection of playing cards, a limited selection of books, and a couple of puzzle-type tricks. As an avid book collector, I was disappointed to only find Mnemomica and the Card College series on the shelves; however, the manager happily brought about 20+ other books from the backroom when I inquired if he had any other books for sale. The manager didn't mind if I carefully looked through the books or playing cards that weren't sealed.

Although I didn't get the chance to check it out, the manager also recommended checking out 'The Illusion Bar' (Cocktail & Magic Bar ILLUSION) in Prague. From the reviews, it seems like a great place to catch some magic while you're in the area. The bar is located closer to the heart of Prague and a very short distance from places you'd visit as a tourist.

Hope this helps someone in the future!

AsL

Too bad I didn't see this thread before my last visit to Prague. That Illusion bar sounds great.

Another shop I can recommend is Butterfly Magic Store by Ondrej Psenicka. It's not a huge shop, but they have a really nice selection of playing cards (Butterfly Cards and others), books and tricks.
When I was there, I was lucky that Ondrej himself was there, he was very nice to chat with and even let me take a picture with one of his Fool Us trophys.