I also made a bakery recently.
You can bake a batch of something and then when you click on it you can click on pick up a serving. That makes the Sim put the single plate in their inventory. You will definitely make more money this way as single plates sell for as much as the whole plate of whatever it was.
The warming rack is also a great investment as you can put items in there and they are automatically put for sale. Oddly enough I kept it in my kitchen and the customers seem to know it's there and they keep trying to get to it but the door is locked.
It's cheaper to just rebake the items rather than restocking but it is time consuming. Getting cheaper restocking as a perk is something to strive for sure. But it's fun just baking and restocking after the store is closed too. ?