The desktop files need to contain %U in the Exec entry if the file contains a "X-KDE-Protocols" line so that it will work. kmail for example will crash if that is not the case while trying to open an office attachment.
This has not much to do with how we package it in gentoo. It is bogus check that verifies that the GNOME_VFS is eanbled and then use %U which is stupid as it should be the case even for KDE. Report this to upstream but nothing buch to fix in ebuild.