I suggest you take a look at this thread on the Unity Forum.

http://forum.unity3d.com/threads/get-all-the-childs-in-transform-even-if-the-childs-are-inactive.99452/#post-650888 

Hope it helps.

EDIT: Little bit of background info. 

http://docs.unity3d.com/ScriptReference/GameObject.GetComponentsInChildren.html

This states you can use the boolean includeInactive behind GetComponentsInChildren to also get the inactive components. This way you can grab all the transforms. Even inactive ones.