I know that the Rulebook pg 18 states, 3) THE RULE OF ACTION TOKENS
No effect can result in more than two action tokens on a character. If an effect would cause this to happen, place action tokens on the character until it has two action tokens and ignore the rest. You can’t choose to use any effect that would cause your character to be given a third action token.

However, does this mean that unless specifically stated, powers/abilities do not deal penetrating damage if the targeted character already has two action tokens? For instance, with the trait (Special) Injustice League: At the beginning of your turn, roll a d6. 6: Give an action token to an opposing character that's 100 points or less. Can this only done against opposing characters that have 0 or 1 action tokens? Therefore, since it does not specifically state "give each hit character an action token. If you can't, deal that character 1 penetrating damage", would using the Injustice League trait against a character that already has two action token essentially do nothing?

Yes, it would do nothing.

Gotcha, thank you for the response