I'm using the retail MM game with the MT emunand and around 5:30 am as the bell is tolling the screen grows smaller and smaller... When the new day arrives it fixes itself but this is still weird. Is this normal?
It's definitely normal. I'm using a retail MM3D cart in a retail N3DS, no mods, 9.0 FW... it does the same thing. As to why? It was a style decision by the game devs once upon a time. To me, it builds anxiety. It's like a reminder than time is getting away.
LOL!
That is something completely normal, it even was there in the N64.
Let's just say it is a somewhat nice touch by the developers to announce the entrance of a new day, that's it.