The most common reason for shutdown problems are background services installed via add-ons that take a long time to shutdown after receiving an instruction to stop, so Kodi reaches a timeout value and has its process killed before guisettings.xml has been fully written. The incomplete xml file is then detected at startup so Kodi substitutes a clean (default) file without the settings you've made. The most common problem things that I've seen delaying shutdown are large docker containers, torrent client add-ons, and some of the torrent based pirate streaming crapware. There is no general LibreELEC shutdown issue on NUC devices else the post count in forums would be notable (they are popular hardware) so it is likely to be something local to your install.
Solve the reason for guisettings.xml and things aren't an issue. I'd also look at hardcoding an edid.bin file (run getedid from the console) as this will negate handshaking issues if they also contribute to weirdness.
In the past I'd say "whatever works for you works for us" when it comes to LE/OE choices, but the longer OE continues to fester without security updates and bad design choices, that statement becomes ever-harder to make.