I suggest you re-read the section in the rulebook about area terrain, and Pete Haines article on terrain in USWD 308 is actually very informative on the subject as well.
With normal area terrain, the actual physical proportions of what is *on* the area terrain base is inconsequential. The only thing that matters is the size of the base and the size classification.
The only thing that City Ruins change is that it has no size classification, so the "top" of the model actually dictates when and where it can be seen over.
Are models allowed to move through solid walls on the city ruin piece if their difficult terrain roll is sufficient?
Yes, models can move through solid ruin walls if their
DT roll is high enough because the actual physical nature of the "ruins" is inconsequential except for the size of the base and in the case of height.
Can a model see another model through a solid wall as long as it's no more than 6" away?
Yes, models can see through solid walls of the ruin if the target is within 6" of the edge of the base (for the same reason as the sentence above).
Can a model see another model through a window on another side of the terrain?
No, models may never shoot through a piece of area terrain to models on the opposite side because the area terrain rules prohibit such an action. This is *not* the same as attempting to see "over" the ruin.
What if the window's top frame is open to air?
This is going to depend on exactly how you are going to play seeing "over" area terrain. If you are using a strict model's eye view, then yes, if you can see an enemy model over the top of any physical part of the ruin model then you would be able to see and shoot him.
However, I believe most people are going to play a semi-magic cylinder style with ruins (given the way the example is given in the
CoD book I think most players will assume this was the designer's intent). I think most will play that a ruin base blocks line of sight up to it's highest point, meaning you'd have to be able to see over the highest portion of the ruin in order to see and shoot models beyond.