Honestly? Just don't forget. Make it part of your workflow. Whenever I'm done with something I'll always unhide mesh elements afterwards to see if I missed something. I don't think there's any script out there that will tell you if you have hidden elements or not though.
You could probably write a simple script very easily that checks every EPoly or EMesh object in your scene and does the "unhide all" command on vert/face level to make sure that every part of every mesh is visible. Not quite the same as a warning, but at least you'd be able to see it.