"emerge mkisofs" only installs the documentation and manpages, not mkisofs itself.. I guess that is because of a compilationproblem, but then the installation should die instead of continuing with the merge...
This should be fixed now (mkisofs-1.13-r2.ebuild, CVS version 1.4). Thanks for the report. p.s. Next time you report a bug, please specify ebuild version.