I had the same problem after installing ReSharper. “Organize Usings > Remove and Sort” and some other shortcuts were missing in the context menu.
You can still invoke the commands (when availiable) via
Edit > Intellisense > Organize Usings > Remove and Sort
To show them in the context menu again (in case of ReSharper causing the trouble) goto
ReSharper > Options... > Environment > Keyboard & Menus > Menus & Toolbars >
Uncheck 'Hide overridden Visual Studio Menu items'