I tracked down the first printed mention of the Theban alphabet for your viewing pleasure. This is p. 597 of the 1613 Zetzner edition of Polygraphia by Trithemius and von Glauburg. (the whole book is available on Google Books. There are earlier editions that have not been digitized).
The Latin text below the alphabet refers to the one on the next page, which is the one used in the Golden Dawn Cypher Manuscript. The text above it means, roughly, “Next is an alphabet from Honorius who was known as the Theban, which magicians used to obscure their follies, as Peter d’Abano said in his major quarto book.”
H. Cornelius Agrippa copied this, but simplified it slightly: “Of this kind of character therefore are those which Peter Apponus [Petrus de Abano] notes, as delivered by Honorius of Thebes, the figures whereof are such, being related to our Alphabet.” (Using the JHP edition from Esoteric Archives.)
No one has been able to find the actual text where Peter d’Abano says anything about this alphabet, though. I suppose that means there’s a very interesting quarto that went missing sometime after ca. 1550.
Wait, what? Their follies? Wasn’t Trithemius a magician, too? Well, yes, but not a stupid one; he was writing at a time when one could still get a very unwelcome visit from certain authorities, ones who might not bother you if you were just recording old curiosities that you weren’t actually using.