Is your Hard Drive getting full? A Folder can store as much as the limits of the Hard drive are so that shouldn't be a concern, right? My Main Zabaware has 57 Folders/Directories and its Ultra Hal 7 has numerous folders and my ConceptNet Folders are also in that under that Ultra Hal Folder. There's still room on my Hard Drive so no worries about my Folder at the moment.
While I'm sure you situation is likely different I think there are some possible options for you.
Why not get a couple of flash drives and copy all of your INSTALL programs to them, freeing up room on your current Hard Drive?
Copy all your MP3, MP4, JPG, BMP, PNG, PDF files that you don't use daily and copy them to Flash Drives as well.
Lastly would be to get a larger Hard Drive or perhaps a large External Hard Drive? They have really come down in price compared to the SSD's.
You just need to think about these options and maybe one will work for you.
