What causes a tube to become deflated on its own?
Sometimes the puncture in an inner tube is very small and the air leaks out very slowly.  This is called a slow puncture.  The classic technique for finding a slow puncture is to immerse the partially inflated inner tube in water and watch for the appearance of any bubbles. 

In my experience even the slowest punctures usually get bigger somehow - I don't know how but I prefer not to wait until this happens so I'll usually fix the tube or replace it.