I'm pretty sure this behavior in the Finder (slow response with large numbers of items on the desktop) was fixed sometime in Tiger, or Leopard, not sure which, but remember reading that was (alleged to be) no longer an issue.
Seems a pretty simple test (well, sounds simple to me
) would be to try exactly what you proposed.
Move all your active folders to Documents, or some other folder in your user folder, or create one just for this purpose (named "Desktopper", or some other name relevant to your use). Make aliases of all your folders, and move those aliases to the locations that you prefer on your desktop. You would soon not notice the slight visual change, and the aliases would be transparent in actual use. You could simply leave it that way, even if there was no noticeable change in the response of your system.
[sidebar]: I do notice that I have such a folder on my Desktop that I created years ago not long after I started using OS X, probably in OS X 10.1 (Puma?), when I had my first iMac. I made a folder with aliases for the main utilities that I used. Some links remain the same (Disk Utility, Terminal, Pacifist), and some have changed as time passed, such as OnyX.
Anyway, I use that same folder, which has survived many updates to both system and hardware. Always sits in the same spot in the bottom right corner of the screen.
I've probably got about 20 other folders (none of which have the "alias" treatment), but I try not to add more if I can help it.