I don't think that Universe Sandbox 2 will ever have too many simulations because, from time to time, more and more simulations are being added as new updates are added.
Developers might modify the interface so that simulations can be organized into folders. I believe that when Update 21 comes out, the interface will change slightly, in a way which allows users to create folders and sub folders so that simulations and saved planets can be organized to a tree structure, like Windows Explorer shell folders.