you gain more experience when you do a non lethal takedown, the bonus is called Merciful Soul
Merciful Soul: neutralize an enemy using non-lethal methods (20 XP)
There are also other types of xp bonus for every enemy you come across, see this postthis post for more information.
To maximize your experience, you will want to do as many double takedowns (none lethal) as possible and normal none lethal takedowns otherwise.
And killing enemies makes more noise where none lethal takedowns are virtually silent.