I did a creepy-themed bakery on my game. My Sims sold things like Zombie Cake, Ambrosia, and Cowplant Essence Pie. There was an upstairs area for the customers and a downstairs area that with an Employees Only door. Downstairs was where I kept the ambrosia ingredients and had the kitchen area. My Sims eventually started selling the Ultimate Vampire Cure as well, so I had a lot of potted plants down there. The cowplant was in a separate room next to the main building. My Sim tried to tell customers not to go in there, but some just didn't listen... ;)
Usually one Sim would be downstairs baking and sending stuff up while the other was selling. I never restocked items except when the founder died and his next of kin hadn't quite worked up the skill levels for the more expensive items.
I honestly didn't realize single cupcakes weren't sellable, as I never tried it. I always made them in batches, and if a Sim took one... well, I wasn't going to try to put a half-eaten cupcake on sale, anyway. ^_^;;
I haven't tried a cafe yet. I'll have to give it a shot. Sounds like fun. :)