I get the feeling sometimes some of its non lethal regardless and you just knock the enemy out much like the cyberphycho's
With the cyberphycho's you pretty much need to deliberately go up to them after you've defeated them and put a bullet in there head to kill them, even if you have used nothing but lethal weapons to begin with, the same rule applies to quite a few "boss" or npc you encounter, case in point the vodoo boys leadership, i thought i wiped them out but a day later i received a message from placide to watch my back, needless to say in subsequent playthroughs once i downed them i then put more bullets in them an recieved no message