Does Deus Ex make a distinction between dead and unconscious?

Solution 1:

The game does distinguish between lethal and nonlethal damage. For example, in the Battery Park mission, if you avoid lethal force, Sam Carter will be happy with you and Anna Navarre will be disappointed. (Note that in this particular mission, if you go talk to Anna, the soldiers at the entrance will attack the NSF and their deaths will be blamed on you. Don't approach Anna at the beginning if you want the 'pacifist' debriefing. This might be why you got the 'necessary force' comment. I'm not sure.)

Similarly, Paul will be happier with you if you don't kill people.

Further into the game, the distinction between lethal and nonlethal force becomes much more a matter of personal taste - there are far less in-game consequences for either killing or letting the enemy live. As tereško pointed out, one consequence is that if you knock a Man or Woman in Black unconscious, their body does not explode.