The 'sntp' binary from net-misc/ntp-4.2.6_p5-r10 is installed into /usr/bin/. it should be in /usr/sbin/. The /etc/init.d/sntp init script will also need to be updated to the new location. This is related to bug #66671 which moved 'ntpd' and 'ntpdate' to /usr/sbin/. sntp is supposed to replace ntpdate so it should be in the same place.
nothing should be relying on the location of the program. so whether it be bin or sbin or the moon, people can find it via $PATH.