When you model as piping, then no stiffness is considered for the piping, the software only adds wind area and weight.  The wind area and weight are assumed to act on the centerline of the main stack, as you can tell since you never enter the orientation or radial distance.  Therefore if the piping becomes large with respect to the Main stack, then this may be a poor assumption.  The software also assumes that the piping is supported by the main riser, and that there are no additional supports.  Additional supports for the piping complicates the situation, and MecaStack can not handle that case. MecaStack also doesn't do any differential thermal expansion analysis, it is assumed to be handled by the designer outside of the software.  Piping is usually anchored at one location, usually the bottom (Anchor attached from main stack to piping) and then the thermal expansion of the piping goes vertically.  There are usually guides (Allowing for movement) between the main riser and stack.  

The wind area is calculated by taking the diameter of each pipe (with insulation) and multiplying it by the shape factor.  MecaStack treats the piping as if all pipes are experiencing the full wind load.  The codes provide no provisions for estimating shielding, and in some codes (i.e. ASCE 7) there is actually specific language the instructs the designer not to consider shielding.  If you decide that shielding is justified in your case, then that is handled by entering a custom shape factor by clicking "Override Shape Factor".  

The total Wind area is calculated as shown in the table below, which is part of the MecaStack output:

The wind load is applied on the stack centerline, the eccentricity is not considered.