There is a slang expression in German: "nicht die Bohne" ("not the bean"), which means "certainly not", "not in the least","not one little bit", "not the least in the world", "don't care at all", and also "not give a damn". (See:https://en.wiktionary.org/wiki/nicht_die_Bohne, Language: A Linguistic Introduction to History, Verbatim, Volume 8, 1982, Nicht die Bohne: zu Thomas Manns Werk Wälsungenblut, The Black and Red - Volume 7, Page 108, 1903, Releases the Silesian Society of Folklore, Volumes 27-29, 1926)
So, reversing these meanings, to say that someone "did a bean" could mean to produce something that was "certainly so" or "in the highest regard" or "what we care about most" or "the most significant". Therefore, it isn't so much about "being smart" as "being significant/important".
This interpretation is tentative, because I could not find any German reference to the phrase translates as "You had a bean" or similar.
Waco, TX is in McClennan County, which is next to Bell County, which had a high concentration of German immigrants from Upper Silesia (now part of Poland). I can not find any connection between Silesia and this particular expression, so it may or may not have originated in Silesia.