ntp, current version and prior does not rely on systemd for any functionality. Having set -systemd in make.conf, it makes sense that systemd support/config files should not be installed. This is unwanted behavior and not the Gentoo way.
see endless -dev@ bikesheds, council decision otherwise.
p.s. if you want to save the 2 inodes you can do INSTALL_MASK=/usr/lib/systemd/system.