Don't think anyone's seen it mention but I finally got KK to appear on my island so I "beat" the game and immediately after getting control of my character again I got notifications that I had completed the Bug and Fish critterpedia after having previously done the All Fish/Bug/Fossil cheats.
So if you did those, and were annoyed they weren't marked as being completed in Critterpedia, it looks like they will once you have beaten the main storyline.
So if you did those, and were annoyed they weren't marked as being completed in Critterpedia, it looks like they will once you have beaten the main storyline.