The ebuild defines datadir=/usr/share/misc which leads to installation of magic* in /usr/share/misc/file/. This deviates from upstream and also from FHS. It should be installed in /usr/share/file/ instead, i.e. the ebuild should leave datadir alone. (I've looked into our CVS history: This datadir definition was already present for sys-apps/file-3.*. At the time that was o.k., since there was only one file, namely /usr/share/misc/magic.)
file-5.00 installs just 1 data file, so ive moved that to /usr/share/misc/ in file-5.00-r1 ...