I'm interested in any answer, but I'm particularly curious if there is a limit on how often you can it for a given store. For the Food store's it is normally hard to keep them stocked, and if I can only get "Fully Stocked" tower bux bonus say once an hour per store, than I wouldn't work as hard to keep those stores full.
You always get the bonus, the issue you're noticing is you don't always get the Tower Bux. You'll note a little (useless) coin bonus at the bottom right every time you fully stock. They actually used to have the same Fully Stocked notification for Coin Bonuses, but it was annoying as heck and they removed it long ago.
The Tiny Tower wiki claims you have a 1/6 chance of getting Bux for fully stocking a store.
Quickly stocked floors like Food floors are easy to fully stock if you're paying constant attention and they'll thus get you the most fully stocked bonuses. Otherwise, just stock stores which you can keep up with at a reasonable place. Quickly stocked floors are hard to keep up with, and it's probably not worth changing your playing style, you'll have to pay a LOT of attention to the game to keep up with <1 hour restock times.
Generally, just don't change your style of play other than always stocking your third items first. Also, Dream Job Bitizens double stock but not stock time or sales, so your stock lasts longer; this means you have 2x as much time to get the fully stocked bonus.
To keep the food stores (in your example) longer, there are only two things you can do.
Spend Tower Bucks to (3 per upgrade) to upgrade the stock level of all three levels. This will increase your stock by 75 items on all 3 levels.
Make your TinyTower citizens happy by placing them in their dream job. That will double the total stock per how many dream job employees you have at that store. Note: This is random when you gain the residents (don't be afraid to evict them!).
Both of these paths can significantly increase your chances for receiving the bonus. [ But from my experience it seems to be random ]
It appears that you always get a fully stocked gold bonus, but getting the fully stocked bonus bux is totally random. Much like getting a tip from the elevator.
This thread shows that it is about a 1 in 6 chance to get bux for fully stocking.