What you need to do is maintain a list of inactive objects so you don't need to use find with tag all the time which is what your problem is.

When you deactivate them do something like this:

var objArray;

function Start(){
   objArray = new Array;
}

... your bit ...

if (exploring == true)
  {
      for(var go : GameObject in GameObject.FindGameObjectsWithTag("zones"))
      {
          objArray.Push(go);
          go.active = false;
      }
  }

Then when you want to bring them back on do this:

while(objArray.length>0){
   var go : GameObject = objArray.Pop();
   go.active = true;
}

Array docs:

http://unity3d.com/support/documentation/ScriptReference/Array.html

Another approach would be to selectively disable the components that a gameObject have, instead of disabling the gameObject. This approach lets you access again the gameObject via the methods you mentioned: GameObject.FindGameObjectsWithTag()

Suppose that you have a gameObject with a Mesh Renderer and a script called myScript. You can set those two object to a disabled state:

renderer.enabled = false;
GetComponent.<myScript>.enabled = false; 

Colliders are more tricky. You can disable them by setting the gameObject in a different layer eg 10.

gameObject.layer = 10;

You should then define in the Physics inspector that objects in layer 10 don't collide with other objects. Physics inspector can be found in Menu->Edit->ProjectSettings->Physics and the place you define the collisions is the Layer Collision Matrix.

Notice that for perfomance reasons it seems to be a good practice to disable all scripts that contain onGui functions when you don't use them.

GetComponent.<myGuiScript>.enabled = false;

A good explanation on why you should do this is here http://www.mindthecube.com/blog/2010/09/avoiding-performance-cost-of-ongui

References:

http://unity3d.com/support/documentation/ScriptReference/GameObject-layer.html

http://unity3d.com/support/documentation/ScriptReference/GameObject.GetComponent.html

http://unity3d.com/support/documentation/ScriptReference/Behaviour-enabled.html?from=MonoBehaviour

(since scripts are MonoBehaviours that descent from Behaviours so they inherit their variables)

http://unity3d.com/support/documentation/ScriptReference/Renderer-enabled.html