My Desktop folder is missing from favorites menu and also from Finder Preferences.
I'm assuming by your Favorites menu you mean in the Finder's Sidebar?

To rectify this:


Go to Finder
Select Finder > Preferences
Click on the Sidebar tab
Make sure the Desktop checkbox is ticked
Exit Preferences


If you mean that the option for your desktop isn't actually available in the above Preferences, try the following as a test:


Open a window in Finder
In the Sidebar, click on your username
In the list of folders, you should see the Desktop folder
Now drag the Desktop folder to your Favorites in the Sidebar


Let me know how you go.