Let me explain a bit my current structure:
The grid on the previous picture is a Level 9 Grid I put every data from one cell into one area-directory. So in one Level 9 folder I find around 6 to 10 airports.
(this looks ok for me, since I will not build all the airfields and airports highly detailed. If I choose one for detailed work, it will separate it.)
A level 10 grid provides the separation of my cultivation so I get four cultivation files in the area-directory.
The cultivation files have 60 to 130 MByte size which should be manageable. The size of one cell is around 27 km so I use a display range of 50 km in the airport referencing the cultivation file. If one level 10 cell does not include an airfield I use a dummy airfield.