If the upgraded character is defending against a Decepticon Leader, does it also get +1 defense from the first ability?
Yes. Both abilities apply. The upgraded character gets +1 defense and the attacker gets their Pierce total reduced by 3.
If the attacking character is a Decepticon Leader but it doesn't have Pierce or it has Pierce 2 or less, what happens?
If the attacker doesn't have Pierce, nothing happens. If it has Pierce 2 or less, it effectively won't have Pierce. A character can't have a Pierce total of less than 0.