Were actually treading into what Id call religious territory here. There are definitely some strong opinions on both sides of this issue.
I actually agree with the article that you found. The desktop should be only for shortcuts, not for files.
Personally, Im not a fan of putting even shortcuts on it.
How files disappear from the desktop
On your desktop, its very easy to accidentally click and drag or otherwise mess up things that are stored there. Thatsprobably what happened with your files and folders. Something unexpected happened and because they were on your desktop in front of you, you somehow accidentally selected and deleted or moved them.
I cant say thats what happened for certain. One of your applications [notably cleanup applications] may have done that, too.
How the desktop works
The desktop is really just like any other folder on your hard drive. It can contain anything: files, programs, subfolders, shortcuts, or other things. But it also has a special property being displayed a backgroundimage and then icons of whatever resides in this special desktop folder.
The desktop was never really intended to be a place where you would put actual data. Instead, youre expected to put files and folders into places like My Documents and programs into the Programs folder. As that article that you mentioned pointed out, the desktop is just a place where youre expected to put pointers shortcuts to other things on your system stored elsewhere.
In my opinion, shortcuts on the desktop still arent all that handy. When youre working in an application, the desktop is hidden, so its difficult to access whats stored there. If you have shortcuts there, you somehow have to make the desktop visible to get to them.
Its easier to use the Start menu; its also why the disappearance of Start in Windows 8 has caused such a kerfuffle. People rely on Start and actually use it properly.
How people really use the desktop
Unfortunately, because the desktop can contain anything, people use it for everything.
I see people filling up their entire desktop with things that it wasnt meant to hold. It can slow the computer down a little, and I know it slows the people down as they try to find whats where on their cluttered desktop. [And heaven forbid that Windows re-arranges the icons on the desktop, which it has been known to do unexpectedly.]
I cringe when I see desktops that are covered with icons for shortcuts, documents, programs, and whatever. I realize that some people are just comfortable with that, but for me, its way too cluttered.
But its not completely a matter of taste. I base my opinion on my 20-plus years of using Windows and understanding how it was [and was not] designed.
My recommendation is simple. Move your documents and data files to your My Documents folder. If you have it as part of your backup strategy, you can also move your files to a Dropbox-linked folder. Whatever you do, you want to move your files off the desktop.
Uninstall and reinstall programs so they end up in your Programs file folder.
If you want to have anything appear on your desktop, create a shortcut.
You can also use the Start menu. Not only can you click the program in the Programs folder that appears here, you can also click Recent Documents or Recent Programs to access the things you use the most frequently.
You can even create you own sub-menus for your favorite or frequently used programs and documents.
Having wall-to-wall icons is not the purpose of the desktop. It can be used for that, but its just too fragile of a place to put files and programs, as youve unfortunately discovered the hard way.