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If you press "ESC" while the plymouth shutdown splash is displaying you will see a countdown of around 1m30s due to some "User session"...

I saw a suggestion to edit /etc/systemd/system.conf and uncomment the two values of "90s" and set them to "10s" and it now shuts down a little quicker

It is not the case that KDE Neon won't shut down, but a 90 second countdown is invoked before shutdown. The solution is simple. Some distros - Fedora 24 KDE in particular - have an icon for Systemd in System Settings, but it is not installed in KDE Neon by default. To rectify this install 'kde-config-systemd'. It doesn't show in Muon Discover but can be installed via Synaptic or running "sudo apt-get install kde-config-systemd" in Konsole. Once installed an item labeled "systemd" will show in System Settings. Activate and open the tab "conf". Find the entry "DefaultTimeoutStopSec (s)", double click on the default setting of 90 and amend to 10, apply and reboot. The change won't apply until after reboot, but then the delay in shutdown/restart is far more acceptable.

(I too tried manually editing system.conf by other means - but it was a major pain and for some unknown reason didn't work.)