Really you should be able to move your scenery folders anywhere you like, provided you add them to the Scenery Library AFTER the move. However some scenery folders, such as the VLC libraries, rely on a registry pointer which allows for an easy update of the library -- shifting this folder will mean that you can't update it properly. So leaving them at the default install location is the best option. Scenery like Orbx which uses an external tool to manage regions also needs to be left alone. (Although they are a good candidate for redirection --- see below.)
I did mention redirects, but maybe these wouldn't be the solution here. This involves making a symbolic link to another location, and it is a good solution for those who use SSD drives, where they want to put FSX and scenery on 2 separate drives.
This has been discussed here.You could do this with individual scenery folders, and I do use it for some, but it won't help you tidy up your FSX folder -- although the scenery folders are shifted, the link still shows up as a folder, which is just as messy as having the original folder.
So the choices are to shift them where you like, but be aware that you might lose some features, such as auto-updates, or leave them where they are and just ignore your FSX folder -- sure, you'll end up with a lot of folders there, but it won't do any harm. Remember that there are plenty of ways to search for particular files or folders.