To first: discrete ports need to be deembed from s-paramters results. It's possible in CST with macros. But just consider the exication, the waveguide uses a TEM or QTEM mode to excite, in a case of discrete port, it's a current and, depending on discrete port setup, at one point, one face or one edge. Nevertheless it's possible to use discrete ports but not very accurate.
To second and third : agree, you can use electrical shielding but till now I don't understand the benefit of using waveguide port inside a structure in comparison with reality.