I've had some issues with passthrough before. Then it did help to disable and re-enable passthrough in the settings. There was a time when this workaround was required in older versions of LibreELEC (or even OpenELEC) - have you tried this?
Please keep us posted about the update procedure and whether it fixes the issues.
I've got a NUC8 i3 hooked up to an old AVR, so passthrough and whatnot isnt an issue for me. But once the AVR kicks the bucket it would be nice to know how to fix this problem.
I have the same issue as the OP.
I am running LE 9.2 on a NUC8i3. I have a wired logitech gamepad that works well, and I can use a Nintendo Wii U Pro controller via Bluetooth just fine.
I can pair a wiimote via bluetooth and it acts fine in Kodi - I can control the menu and playback alright. In Retroarch it shows up as a controller, but none of the buttons have any effect. Not in the menu, or in any cores. (I have tried several Mame and Nintendo cores).
My next step is to replicate the issue while viewing the debug log to analyze it in detail. Since wiimotes are rather common this surprises me somewhat.
You could try the dual-audio patched versions, someone kindly has made builds of LibreELEC made available here: Index of /LibreELEC-DualAudio/Generic.x86_64
I'm running such a build on one of my boxes. But I do get a slight audio delay, depending on the combination of codecs and inputs. YMMV.