One reason they are not documented is that if you use such hardware registers directly you make your program non-portable - ie it will only work on say ATmega328-based hardware. The higher level Arduino interfaces/libraries are designed to be as hardware-independent as possible(*) and you are encouraged to stick to them unless you need the extra performance or facilities that direct hardware access can give.
Another reason they are not documented is to keep things nice and simple for newcomers and non-specialists - the details are hidden behind libraries for the most part.
(*) there is a limit to how hardware-independent you can be on a microcontroller of course - even moving between Uno and Mega involves obvious porting issues.