Yeah, when you muck with resolutions, the system has to rearrange things on the desktop to fit the new resolution, even if that resolution is only temporarily there. Then when the resolution is restored, the system again calculates where things need to be, not where they were when the the screen was that resolution last time. And that shuffles things all over the place.
Yes I keep a lot of icons on my desktop (which is three monitors wide BTW). All sorts - files, folders, aliases, and weblocs. Rather than drill down to find what I want I sort of work like a lean desktop, knowing the thing I am looking for is over there and just reaching for it.
I know we all work differently, but this is a particularly inefficient way to go, I think. I would not use "lean" to describe a screen full of things all over the place. But some folks are very visual, like my wife, so her Desktop is cluttered as well. I have my Desktop somewhere between minimalist (Little to nothing on it) and hers (stuff covering 3/4 of the screen). I do have 10 external drives attached, so those icons are there, along with a dozen or so folder or aliases for folders that I use frequently. I periodically purge the desktop of stuff I dropped there for convenience, just as I do on my real desk. Not totally clean, but not cluttered.
The only time a cluttered Desktop actually impacts performance is at boot time when all of the links and icons need to be created and place on the Desktop. Other than that, Desktop is just another folder to the system. So, you do what you want/need. Good luck reorganizing it all. One thing you might do is take a screenshot of it once everything is in place so that the next time you have to redo it you have the pictures to follow.