Rebooting every night is a like a band aid. If there is a memory leak somewhere it should be fixed.
Get us a debug-enabled full kodi.log (via a pastebin site), perhaps we're overlooking something obvious. Which skin?
Will the log be saved when kodi freezes? I will enable full debug log and when it freezes again i'l upload it.
I'm using the Estuary Mod V2.
The strangest thing is i only have the freezes on my RPi3. I'm having the exact same setup (backup/restore) on a RPi2 running in my bedroom without any problems.