Thanks for the info!
This is very puzzling. Systemctl start atvclient does exactly the same, it runs atvclient -m, and no errors are logged. No idea why one invocation should work but not the other.
You could try playing around with the Harmony settings. A lot of IR issues stem from the Harmony working quite differently than original remotes. For example, command repeat should be set to 0. Another thing to check is the configured remote profile - there are 2 different apple remotes, see eg here: Apple remote - Official Kodi Wiki . Try both the 6 and 7 button remote profiles.
If none of this helps, it's worth testing with lircd instead of atvclient. First disable atvclient:
then reboot (you can later re-enable atvclient with "systemctl unmask atvclient" plus rebooting).
Now copy /etc/lirc/lirc_options.conf to /storage/.config/lirc_options.conf and change the driver and device configuration:
driver = macmini
device = /dev/usb/hiddev0
Note: if you have more than one /dev/usb/hiddev* file, test with all of them.
You'll also need a /storage/.config/lircd.conf file matching your remote. You can either try the one from the kodi wiki page linked above or this one - depending on which remote you have configured - lircd.conf.macmini
If you use the latter you have to change the KEY_... definitions to KEY_UP, KEY_DOWN, KEY_LEFT, KEY_RIGHT, KEY_OK and KEY_BACK to get normal control.
Now you can enable Lirc in LibreELEC Settings -> Services and see if it works.
If none of the lircd.conf files work, you can try to create your own using irrecord. Make sure you disable lirc in LE settings before, otherwise irrecord can't access the IR receiver device.
irrecord -H macmini -d /dev/usb/hiddev0
After running that copy the newly created REMOTENAME.lircd.conf file to /storage/.config/lircd.conf and enable lirc in LE settings again.
Note: I haven't tested this myself (don't have the hardware), so it could be that I got something wrong. In this case just post here 
so long,
Hias