The qt flag in the media-gfx/graphviz-2.28.0.ebuild is misnamed, it should be "qt", not "qt4", since the ./configure option is --without-qt. I changed my local copy of the ebuild (replacing qt4 with qt) and it emerged as expected.
I can confirm this, and it's still not fixed in 2.38 (2 years later).
fixed in 2.38.0-r1