How to identify or calculate the electromagnetic interference (EMI) contribution of components on PCB
My question how do we measure the EMI contributed before and after the addition of the bypass and decoupling, grounding control, transmission line control, and trace termination matching ?

Yes, you could use a Electromagnetic Finite Element (EM FEM) to model the noise on the PCB. ANSYS and Comsol make programs that can simulate noise sources and EMI, one can even import a 3d model and see how a noise source would propagate noise on and off the PCB. However these programs are usually more time consuming to use then actually building and testing a PCB. Because of this I build and test since I have to test prototypes anyway.

Is there a theoretical way to determine or predict this ?

A good start is this book, (since there is more information on EMC that you request than can be posted in an answer). Chapter 5.2 describes transmission lines.
Chapter 6 describes shielding.
Shielding is probably what you want to do, since if the IC or the PCB is radiating, a shield can help you meet FCC regulations.
Another problem is radiation emitted from cables, ferrites and adding inductance can stop cables from radiating.

Source: http://www.hottconsultants.com/EMCE_book_files/emce_book.html (no affiliation, except I own the book and think it's great)