The First Known Book-Covers with Magen Davids are:
”Beur al sefer Shaarei Dura” by Rabbi Joseph Ben Rabbi Moshe from Kremnitz, which was printed in Prague in 1609. In a similar design were issued in Prague in 1611 the books " Imrei Binah" and “Mekor Chokhmah".
Thanks to Eli Eshed, journalist who calls himself a "culture detective", for directing me to this piece of information.
Daniel Putík from Flickr:
Just to let you know that a Magen David does appear on the front page of a Siddur printed in Prague by Gershon Ha-Kohen (Katz) as early as 1512. Unfortunately, I can not find a picture now. My father wrote a study about this. Alexandr Putík, "The Origin of the Symbols of the Prague Jewish Town. The Banner of the Old-New Synagogue. David's Shield and the Swedish hat“. Judaica Bohemiae vol. XXIX (1993).