No, the eye candy provided by Aqua is what makes up the look of OS X. The engine used to provide the GUI is Quartz, which is closed source from Apple. Apple does have an X11 that can be installed on OS X in order to run programs that use X Windows on OS X, like OpenOffice or GIMP.
Software Update is just one of many graphical tools used by Mac OS X. Software Update updates anything in Mac OS X that needs to be updated, whether it be a UNIX command or process or some high-level GUI application. It's all integrated into one package that is OS X. Of course, this only updates software that was made available on your OS X system from Apple. In other words, if you have something like Firefox on there, Software Update won't perform updates to that program since it wasn't originally included with the operating system. However, Safari and other Apple applications are updated through there, and you can manually download those updated from Apple if you choose to do so.
Consider Synaptic, which is a graphical front end to apt-get in Debian-based distros. This not only updates the low level stuff that might be commadn line based if it's an application, but also the stuff X11 uses and even X11 itself, as well as the desktop environment used. Same thing with Software Update.