To be able to see the buildings/enter them, for the bridges to be visible, and for the town center tree to be visible/also be able to sit on it's planter. You are not able to go inside or interact with any of them either.
I'm able to recreate this on my hardware consistently, though. This isn't consistent though as other users have reported this not working. The train station, which is the building you come out of at the very start of the game, will usually appear if you don't have the "00086400" save folder for ACNL, but if you do the train station will disappear and cause a soft-lock at the beginning of the game (no further events happen, but animations (idle in this case) continue). In the previous issue some people were reporting that buildings will show up sometimes, but the conditions of which they do are unknown.
This happens IN-GAME though, the buildings are visible on the title screen, just not once you enter the game. These are real emulators however, the emulations are nowhere near perfect, as there are still some elements not yet emulated that certain games utilize or require, and the hardware on it is still not fully understood.
Collisions do work correctly though as you seem to walk into an invisible wall where these 3D models are supposed to be located. Unlike in previous Animal Crossing games, where you had a single dedicated recycle bin found inside the Civic Center, in New Leaf you can place trash cans in your village. The official Citra compatibility list can be found here Currently, there are four real Nintendo 3DS Emulators: Citra, 3dmoo, TronDS and XDS. In Animal Crossing: A New Leaf buildings, bridges, shops, town hall, and the town centers tree are invisible and don't allow interaction (such as going inside of a building, sitting on the tree planter, etc.). Log From Beginning Until Running Into an Invisible Villager Building (Nightly): and hopefully in a format easy for a dev to go through. The initial issue for this was getting a bit off of the trail and the beginning post didn't quite have a very good gathering of what the issue was to keep things simple, so I'm recreating this here to put in what I've solidly tested out.