All Havdala Bsamamim boxes I have ever seen are in the shape of a tower.
Why (and when) did it take on that classical shape (rather than just a silver box)?
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This article, by Rabbi Shubert Spero, says that the fashion started around the sixteenth century.
He suggests that a tower symbolizes strength and security, and so it fits well with Havdalah, in which we speak of Hashem as our source of security ("כי עזי וזמרת י-ה"), and also that it is associated with the rebuilding of the Beis Hamikdash and the coming of Eliyahu and Moshiach, a major theme of Motzaei Shabbos.