Try condensing your scenery by area;
ADDON SCENERY / NORTH AMERICA ... and put ALL the .bgl's for airports in NA into the scenery folder, and all the textures in the texture folder.
Addon Scenery / South America
.. / europe
..... do it pretty much by continent.
(granted you loose your ability to turn on / off individual airports/LOD's/ MESH's and such, but it will clean EVERYTHING up a bit faster.)
...that's the bit that stops me doing it that way....makes fault finding harder!
All the Folders in my Library are individually named for easy access...

...but it makes the list VERY LONG...

...!
Paul,,,G-BPLF...FS 2004...FS Nav...and a long list...

...!