The short version is that "counterstrike" is a trait that an attack has, like Piercing, Unavoidable and so on.
gaining Counterstrike again doesnt do anything, because the attack already has the "counterstrike" trait.
For example, Brogan has Unavoidable naturally. So if you played Perfect Strike on him, the second instance of Unavoidable doesnt do anything because its not a stackable trait (as opposed Piercing, which does stack). Thats whats happening with multiple instances of Counterstrike.
All of the Hydra's quick attacks naturally have that trait, so when it guards its quick attacks gain a trait that they already possess. Revealing Retaliate also provides the Counterstrike trait, which any blocking creature gained for blocking.