To be honest you are confusing me, but I think you may be missing an important point:
You cannot drag select a prefab from the library into an action for an object in the scene, unless it's a simple Create Object action.
So you can say "create X prefab object from library", but you can say "get the position of X prefab that isn't in the game yet" or etc.
However the prefab object itself can see and communicate to it's children. The easiest way to set this up is like this:
* Place the prefab in your scene
* Edit that object in the scene. Playmaker will say you are editing a prefab, say edit instance.
* Drag select it's children from the scene and not the library
* When you are done, use the apply button in the Inspector to make the changes to the object in the scene apply to the prefab
If you do it that way, you will avoid any confusion about what is being changed and how parts are being identified.
As far as Activate Game Object goes, that certainly won't work. The object isn't just disabled if it's in the game library, it's flat out not in the game (scene) yet to even turn on. You would have to instantiate it (create object) to make it in your game, and thus able to have a status such as inactive or active.
The answer to you ultimate question (that you didn't ask) will depend on what exactly you are trying to achieve, not how you are currently trying to achieve it.
When you are trying to activate a child object, is this expected to occur to multiple instances of the prefab that are currently in the scene? Or is it for just select instances of the prefab, and others in the scene aren't meant to be effected?
I think maybe the best place for you to start is describe what you want the game to do, and then everyone can help with suggestions on how we would do that.