I have only had our site working for 3 weeks but I made a file with over 15,000 airports and it slowed it all down.
So I slimmed them all down, if the airport is not in the system it will add them as it goes if the system can look them up. Its best to keep the file as small as you can get away with.
The same with flights, our old website had 4000 flights which caused all sorts of problems.
regards
Doug