we cann't exculde the influence of electrodes on whole device!
Yes, so the modeling you should do depends on what you want.
For instance, if you want to investigate a contact resistance between electrodes and molecule or the influence of electrodes against the electron transport properties more accurately, you should prepare 3D electrodes.
On the other hand, if you want to focus mainly on the intrinsic electron transport properties of molecules, using virtual electrodes may be permitted.
how can we assure the sense of periodic boundry at X,Y direction if we use the virtual electrodes which have large padding region!
In such a case, periodic boundary condition is not indispensable but only an option.
Using Neumann boundary condition gives the same result as periodic boundary condition if the cell size is enough large.