Corey -
These are separate things.
You can purchase UPC codes from brokers and then just print them directly on your labels or print UPS labels and stick them on your packaging. You don't need inventory management software to do that.
I am not exactly sure why you are focused on scanners that connect to a PC. You certainly don't need a barcode scanner to track ingredients for recipes. What you do want is lot traceability and the ability to calculate the cost of a recipe based on what is spent for a particular batch of ingredients, not what you last paid.
I was recently introduced to a service from a company called Mobia Solutions ( www.mobiasolutions.com ). I would check them out to see if they can do what you need. There are also some really helpful resources under the Links tab on food safety, labeling, and more.
BTW, you probably qualify for a small-business exemption to the FDA nutrition labeling laws - but you do need to apply for it if you haven't already.
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clay - http://www.thechocolatelife.com/clay/