There are many advantages. The advantages actually outweigh the disadvantages.
- Untrustworthy scripts will run as the user and not as the web-user (nobody/99);
- Mail script exploits not running as nobody/99.
It's more, "If a hacker hacks you, he will not have access to all user directories, anonymously."
Basically, since the public_html/ folders are user:nobody, well, that means "nobody" can read/execute in the folders... so someone who exploits via XSS (Cross Site Scripting) could potentially find folders that are owned nobody:nobody or that are 777 or 757 or 775 or some combination of permissions. Then they can upload scripts, exploit, etc.
Worst case? Weak kernel, upload script, execute via the web, elevated privilege, owned box. It happens really quickly. The stupid thing? Mostly script kiddies do it, but, it happens quite a bit. I had to clean a box that had 3 rootkits on it just last week, very bad.
Regards,