RE: Fluid Dynamics question
In my opinion, picture 2 without the lower outlet would be a better configuration. Air does not like to make a ~180 degree turn. It would much rather continue on the same path that it is currently on. Also, you are wanting the air to pass over the colling fins. If it doesn't need to pass over the whole engine, then don't let it.
If you do end up going with an outlet at the top, use a NACA duct. These are a lot more efficient than having just a hole.