Apk files have respective odexes that devs use to supposedly save space. Deodexing means you convert it back to a .dex file and put it back inside the apk. This allows you to easily replace files (not having to worry about odexes), but the main point was to deodex services.jar so that you can change all text to different colors (such as the clock color to white) and to deodex services.jar, you need to deodex everything.
If you use SBF then it will be like you never modified the unit so you will have to root again and if you want to run any custom themes you will have to either deodex or load a rom that automatically does it for you.