At a certain point in time, you will hit 'The Barrier'. This is when your shops sell so fast that you're re-stocking every 30 minutes or so! This happens early on when your shops have tiny capacities and you can only stock 10k goods.
The solution to this is the Just In Time skill, acquired when you reach the Roadshow phase. This lets you expand your Capacity or SFR as its known. My little piddly 10k shop now stocks 37k items. Whew!
Note, however, that it is okay to run empty! As long as you turn a profit each day.