When I look at the properties of my LR catalog, it shows 11,000+ files and 18,000+ folders. Why so many - at least 7,000 - empty folders?
If you refer to the xx.lrdata folder structure, it is the previews structure which probably has some pyramid structure in there as well for the different zoom in levels.
I have to check my master catalog, but on a test catalog i happend to check almost all (leaf) folders contain a file.
I usually import images with a 1:1 preview, perhaps that makes a difference.
Nevertheless, i care litle about the .lrpref; as long as it functions i leave it alone.