Why is xprop -root not returning _NET_ACTIVE_WINDOW

You are asking five questions here, and might be better asking five questions ☺ But I'll jump in:

1. X is a server and can be compared to a "web server" in that it is a process that listens for incoming connections that speak a particular protocol (the X protocol) and it issues answers. The connections come from X clients, which may be on the local host or on a remote host accessed over a network.

2. X11 is a "major version" of the X protocol, which has evolved since inception. X11 is the most recent protocol and the most common. (Xorg is an implementation of an X server, X libraries and a collection of clients, all talking X11. There are other implementations: the largely defunct XFree86; commercial ones such as Hummingbird Exceed; forks such as XQuartz, which runs on Mac OS X)

3. A "window manager" is an X client which manages windows. It typically has the responsibility to decorate windows with bevels/borders, drop shadows, a menu bar containing buttons, etc. -- and handle the logic of window placement; support windows being dragged, resized or re-arranged, etc.

4. X requires input and it has a shared responsibility to manage that with the Kernel. Historically, X did a lot of hardware management itself. In modern times, on the Linux platform, X is gradually becoming "smaller" and delegating this responsibility to the Linux kernel. The advantages of this are: smaller X codebase; fewer "crossed-wires" with the kernel and X both trying to manage the same stuff. (an example of this is the Linux event interface, where events from mice etc. are interpreted and translated by the kernel and its drivers into the standard interface at /dev/input/event*, which is consumed by the X server). Note that on other platforms (BSD, Solaris) X is still quite monolithic.

5. There are many, many ways for processes to communicate with each other. I believe X clients can interact by way of the X protocol (for example, traditional X window managers need to know when other clients draw windows, in order to decorate them; pagers need to know when a window's size or position changes, in order to reflect that in the pager). D-Bus is a modern inter-process communication (IPC) technology developed to address the shortcomings of other methods. It is not X specific.

Most modern applications, including all Gtk (→ GNOME) and Qt (→ KDE) applications, use xft, which performs the rendering client-side and sends an image to the server. (Possibly via the XRender extension, but it's an image that gets sent for rendering, not text). So for these applications the X server has no notion of fonts. You can't do any better than checking whether the application has (had) the font file opened.

Even for old-fashioned applications that use server-side fonts, I don't think there's a way in Xlib to query which fonts another client is using.