You raise some good questions, zespri.
Firstly, I have many shortcuts on my desktop, not thousands cluttered, but 15 odd ones within fences. When it comes to default Windows desktop icons however, I dislike the shortcut overlay and prefer the functionality of the default icon. Besides this, there is no way, as far as I am aware, of turning off/on selective shortcut overlays and turning them all off would cause me a migraine, naturally. To answer your question more thoroughly, I like order to my PC. I'm compulsive about it. 
Having said that however, I'm quite happy to wait for Stardock to include fences support for the standard control panel icon if possible at all. It's the only one of the default icons that disappears when double clicking the desktop, a minor annoyance, but worth waiting for an official report on the issue.
Cheers and thanks again,
Paul.