If it is neutral / neutral hostile it will show up on the minimap if you do not remove both patches to minimap icon and model located in the "Advanced >> Game Interface..." Doing just and only this would prevent all neutral buildings from showing the yellow house on the minimap.
It would now be treated as a normal building, as such showing a black square. If this is what you don't want to see, go to the object editor and there is a field called "Stats - Hide minimap display". Set this to true.