AFAIK the main functional difference with a li-ion battery is that it can take more charges and it has no memory like ni-cad batteries do. So, it's okay to recharge early etc.
AFAIK all li-ion batteries in e-cigs are protected. You might have heard about cell phone and laptop batteries exploding. These are the same kind of batteries. The protection circuit keeps this from happening. If you get into mods that use generic batteries, it is important to get protected batteries.