The top layer has a couple of cuts for camera and display DSI to go through. The bottom has a couple of vents.
Honestly, as an exercise I have been monitoring my Pi3 today, no heatsink, and the temperature did not even reach 60 degrees. Sure, I did not stress it hard, but my opinion is that it's a non-issue, whether you encase the board or not.
... now if you overclock it and run Quake III on it for hours, then sure, heatsink and maybe custom case may be advisable. Any other case, apart if you fit a HAT such as the Unicorn that will generate additional heat, nope.
EDIT: of course I'm not considering hot climates and extreme conditions, which may call for specific measures.