Does the build succeed when you put the line
-- snip --
#define HasFreetype2  NO
-- snip --
into xc/config/cf/host.def ?

xc/config/cf/hotst.def doesn't exist.
So I created it, put "#define HasFreetype2  NO" and rerun again. This time the
compilation was successfull.

However, I believe that Freetype 2 is installed on my system:
clock@beton:~$ locate freetype2
/usr/local/include/freetype2
/usr/local/include/freetype2/freetype
/usr/local/include/freetype2/freetype/cache
/usr/local/include/freetype2/freetype/cache/ftccache.h
/usr/local/include/freetype2/freetype/cache/ftccmap.h
[...]
clock@beton:~$ locate libfreetype
/opt/openoffice/program/filter/libfreetype.so.6
/usr/local/lib/libfreetype.a
/usr/local/lib/libfreetype.la
/usr/local/lib/libfreetype.so
/usr/local/lib/libfreetype.so.6
/usr/local/lib/libfreetype.so.6.3.3
/usr/X11R6/lib/modules/fonts/libfreetype.a
/usr/X11R6/lib/modules/libfreetype.a
clock@beton:~$ freetype-config  --version
9.3.3
clock@beton:~$ which freetype-config
/usr/local/bin/freetype-config

Also I remember installing freetype2 at least once in the past from sources
(manually) according to their README, do not remember deliberately deleting
it, and various programs with freetype support (mozilla, gimp, gtk etc.) work
for me from which I infer my belief that freetype2 is installed on my system.

Neither freetype2 nor X.Org README AFAIK presents any official procedure to test
arbitrary running system for presence of properly installed freetype2, so
that my subjective beliefs are the only thing I am able to offer :(

Moreover, freetype2 is not listed among prerequisites for compilation of
X.Org server in the BUILDING file. Only fontconfig is mentioned which I assume
is different project from Freetype2. So I am surprised by the fact that
the compilation is dependent on it.

I have removed freetype2 completely from the system and installed brand
new again (2.1.9) and the problems persists (without changes to
config/cf/host.def).

The problem happened in lib/fontconfig. lib/fontconfig/Makefile reveals
FREETYPE2INCDIR=/usr/include
This is the problem. It should be
FREETYPE2INCDIR=/usr/local/include
because freetype2 on my system is installed in /usr/local prefix.
My installation seems to be OK:
1) freetype-config --cflags reports /usr/local prefix
2) pkg-config --cflags freetype2 reports /usr/local prefix
3) /usr/local/lib/pkgconfig is included in system-wide environment variable
PKG_CONFIG_PATH

So it looks like XFree86.Org have two bugs:
1) the BUILD file in toplevel doesn't mention freetype2, although it seems to be
a dependency.
2) the BUILD file should either specify that freetype2 must be installed in /usr
prefix, or X.Org should test what prefix it is installed in.

This needs to be clearly documented for the 6.9 release.

Examples have been added to xorgsite.def and instructions added to the BUILD 
file in CVS head for the upcoming 6.9 release.   Closing as fixed.