That's an effective way to avoid missing files, but it does eliminate some of the most powerful file management tools on your computer (e.g. Finder, Explorer).
There's nothing inherently wrong with missing files, and nothing wrong with moving files outside of Lightroom, so long as you know you're doing it and know how to tell Lightroom what you did.
Anyway, if you right-click on any folder and choose Synchronize, you'll find a handy button for "Show Missing Photos".