Oh dear !!! That sounds like you have a “pre-systemd” OS ie Raspbian wheezy (or Minibian?) and the “mqtt_input” init script has been removed by the update script perhaps (See the “EmonPi problem after update” thread for more info)
I think that would have probably been before Glyn switched out the mqtt service from SysV to systemd (see the “Mqtt_input script run as systemd instead of initd” thread for more info).
That’s a shame, it would have shed some light on whats what,
Can you tell us the response to
ls -la /etc/init.d/mqtt_input
and also
ls -la /var/www/emoncms/scripts/mqtt_input
EDIT - and what is returned by this command too
ls /boot | grep emonSD