Hi,
Since you already have code that correctly determines if a window residing in a linked model is hosted to an exterior wall, you could put all these windows' elementIds in an elementIdSet, then get the 3D view element and use
View.HideElements (System.Collections.Generic.ICollection<Autodesk.Revit.DB.ElementId> elementIdSet) or
View.HideElementsTemporary (System.Collections.Generic.ICollection<Autodesk.Revit.DB.ElementId> elementIdSet)
Regards
Felix