The ebuild for qt-docs installs it's files to / and not to /usr/qt/3. Just move the line with QTBASE=/usr/qt/3 from pkg_setup to src_install.
We've done it for now, but pkg_setup() was "supposed" to work. In fact it did in all the previous qt-docs ebuilds. To be investigated...
*** This bug has been marked as a duplicate of 5251 ***