So, the traditional Star of David (or Magen David) has been used for quite a while, before the First Zionist Congress. I believe it was also considered the symbol of King Solomon's signet ring/seal in the Muslim tradition, which is why you have examples of the star used in the flags and banners of Muslim emirates. I believe it does have some significance in Japanese semiotics(symbology), but I'm not exactly sure what for.

So the source I'm using is Max Diamont's Jews, God and History Chapter VI: The Prince and the Yellow Star.

So firstly, it should be said that it was first instituted by the Bohemians (Czechs) in the 1300s, as the flag of the Jews of Prague and Bohemia, this was around the same time when the 4th Lateran Council made specific requirements for Jews, specifically canon 68 made a requirement for Jews and 'Saracens' to be distinguished by their dress. The 4th Lateran Council was also the reason for the Jewish Badge, a gold circle. The Gold Star was used with Jewish flags and symbols between 1350-1500 in Bohemia and Hungary, designated or allowed by local monarchs (specifically Charles IV of Bohemia and Matthias I of Hungary).

I also checked, and the Megan David is mentioned as the symbol of Jews in the 1896 book, "Der Judenstaat" by Theodore Herzl, a year before it was adopted by the Zionist Congress.

Edit: You can see how the use of it, not only in Kabbalah but in Austro-Hungary states (Hungary and Bohemia) may have influenced Theodore Herzl and the First Zionist Congress in adopting it in their flag. Herzl himself being Viennese, and the majority of Jews representing the congress being Ashkenazi. This is however, a little bit of speculation on my part.