Once per week on Sunday night. Weight is the way to go for most things. But per container for beverages or per case for slow moving items is fine. As an example, we sell jalapeno poppers but not at a huge pace. We inventory per case so my manager just counts cases in the freezer and estimates the portion of the open case remaining.
Estimating open containers on the line is fine. Guessing wrong by a pound on something is not going to throw weekly numbers off and the wrong guesses will tend to offset each other. For example, I know that 5 lbs of pepperoni fits in a 1/3 pan. If that pan is untouched in the walk-in that is 5 lbs. If it looks about half full on the line that is 2 or 3 lbs. Being off by a pound is about $2. Against weekly food cost that is just not an important number and taking a bunch more time to perfect the number accomplishes nothing meaningful.
For arguement sake lets say you used 3,000 in food on 10,000 in sales for a week so cost was 30%. If your count was off by $20 net one way or the other (remember, your mistakes in estimates will tend to offset each other) you come in at 29.8% or 30.2%… it just does not matter. A much bigger issue is keeping your pricing up to date. If cheese changes by 5 cents per pound and you have 1000 pounds in the walkin and do not update your cost for inventory value that difference is $50!
If you have a specific issue like cheese usage, go to every night counts for that single item, but don’t bog yourself or your manager down with 30-40 minutes of pointless work every day! Similarly, box count is a great way to look for employee dishonesty. If pies are going out for cash when you are not around, the box count will be off. There will always be a few mistakes etc, but if you see that count being wrong consistently, go to every day box counts reconciled with sales.