Here is what I found about the origination of the 'Blackshirts':
The Husker defense is known by the nickname of the "Blackshirts." Depictions of the Blackshirts often include a skull and crossbones. This nickname originated in the early 1960s and continued as a reference to the black practice jerseys worn by first-string defensive players during practice. This tradition developed when Bob Devaney had Mike Corgan, one of his assistant coaches, find contrastive jerseys to offset the red jerseys worn by the offense in practice.[9] Further credit is given to George Kelly, Devaney's defensive line coach until 1968, who frequently referred to the top defensive unit by the name; eventually the rest of the coaching staff caught on, while the first mention of the Blackshirts in print was not until 1969.
I couldn't find anything about the 'throwing bones' gesture though. However, I'm leaning towards the Peters boys back in the 90's starting that gesture.