It's so that you don't just aim for the heads I believe only on punter days so that you don't scare them off hitting them in head might make them not want to come back. So they make head shots not count in a hope that you won't headshot
No, it's so they stay in the game longer and shoot more paint and spend more money
If headshots count, punters spend a lot more time totally hidden behind cover and games see lots less paint used up - if gun and head shots are counted, people tend to shoot more, and keep their guns / heads out of cover more.