Maybe I misunderstand what you mean, but Windows Explorer is also the shell on Windows (handles things like the task bar and the desktop icons), so you will always see it running in the background.

Windows doesn't need explorer to actually function, it's just another component that adds optional extras to the desktop environment such as the task bar and desktop icons. Kill explorer.exe, your desktop and taskbar disappear, but programs still operate and can be manipulated and minimized, just in a more Win3.1 style flavor. A file browser window can be called directly without the explorer shell running, "explorer.exe /e".

Problem occurs when you have programs that dip into explorer's shell components expecting them to be running when that might not be the case. For that case you couldn't fully turn explorer off if you were, for example, trimming down a modern version of windows.