I'm trying to learn this basic thing about processors that should be taught in every CS department of every university. Yet i can't find it on the net (Google doesn't help) and i can't find it in my class materials either.
Do you know any good resource on how addressing modes work on a physical level? I'm particularly interested in Intel processors.
Start on the Wikipedia Virtual Memory page for a bit of background, then follow up with specific pages such as the MMU etc. as to satisfy your curiosity.
You will normally go in detail over all of the above concepts (and some more, such as pipelined and superscalar architectures, caches, etc.) in any decent Computer Architecture course, typically taught by the Faculty of (Electrical or Computer) Engineering.
You might want to take a look into the book "Modern Operating Systems" from Tanenbaum.
If you are interested in the x86 architecture the Intel Manuals might help (but they go really deep)
This page might help. I did a search for HC12 addressing modes since that's what we learnt with, and it is MUCH better to learn on a simple processor rather than jumping into the deep end with something like an Intel processor. The basic concepts should be similar for any processor though.
I wouldn't imagine you'd need to know any of the more complicated ones in an introductory course. We only really used the basic ones, then had to explain a few of the others in our exam.
You should be able to see what's going on on a physical level from that provided you understand the assembly code examples. The inherent addressing command inca for example is going to use a set of logic gates within the processor (http://en.wikipedia.org/wiki/Adder_%28electronics%29) in order to increment register A by one. That's all well and good but trying to understand the physical layer of anything more complicated than that is just going to give you headaches. You really don't need to know it, which is the whole point of using a microprocessor in the first place.