There is circumstantial evidence that Quantrill's lieutenant Andy Blunt used a "nomme de guerre" to hide from justice for crimes he evidently committed in the frontier army out West before the war.
I think other guerrillas used fake names to protect their families.
The one I could never identify was "General Crabtree" of south Cole and Miller Counties at the center of the state. He recruited southern men there and led them to the Arkansas border where he turned them over to established Rebel commands during 1861 and 1862 before local EMM killed him in late September. I nailed down much detail about the man--details of his activities, his death and burial--but not his true name. I even exchanged emails with a local man there who claimed to know "Crabtree's" name, but felt he should continue to protect it, for unspecified reasons. I had no choice but to accept it, but that one's definitely on my "unfinished business" list.
Bruce Nichols