Those are actually very good questions, at least to me as one who has delved into these issues. The answers to a large degree depend on whether we are talking about large companies, like the major chains, or small, mom and pop operators.
One of the best ways for the large operators, such as the chains, to protect their proprietary information and trade secrets is to use a commissary model. Papa John's and Domino's uses such a model, but you don't have to be a major national chain to do so. Regional chains like Papa Gino's and Pizzeria Regina in the northeast also use that model, and I have read of a couple of instances where such a model was used for only a couple of stores. The advantage of that model is that the employees in the company stores, who are most likely to be the source of leaks of trade secrets, whether innocently or intentionally, are kept from access to proprietary or trade secret information. As a result, they are essentially only pizza assemblers. I have confirmed this on my own by asking employees of a few chains about the ingredients that go into their products, dough ball weights, etc. In all cases, I was told that they didn't know. And, since most such employees are low-cost help to begin with and don't stay around for long, they could care less. Some of the chains are also more secretive than others as to what goes into their products. Domino's is the most revealing and Papa John's and Little Caesar's are the least revealing, although both do provide Nutrition Facts at their websites.
It also helps if the operators use proprietary products, such as flours milled to their specs or sauces put together to their specs, and also to package such products in a way as not to reveal much, if anything, about the source. For example, Godfather's and Jet's use proprietary flours. The Jet's flour bags bear labels like "Pizza flour" and their cans of tomatoes are labeled Jet Fuel. But, sometimes, some of the proprietary information can leak out. For example, some schools that have purchase programs with pizza operators require ingredients and/or nutrition information from their suppliers. It was from a public document of one such school that I feel that I was able to determine the ingredients that go into the Jet's dough and the source of their tomatoes (I believe it is Stanislaus).
Suppliers to pizza operators also help protect their customers. For example, when I approached General Mills with the code for the GM flour that Godfather's uses, I was told that the flour was a proprietary blend and could not be revealed to me. Also, when I once approached Leprino's for nutrition information on their basic cheeses, which I could not find online after extensive searching (it is not on their website as it is at Grande's, for example), they would not give it to me as a non-customer of their products. Using private labelling, such as used by Malnati's for its canned tomatoes and its flour, also helps protect their proprietary information. That is not unusual. Many pizza operators trek out to Stanislaus in California solely for the purpose of creating their own signature sauces. Occasionally you will find a supplier or a food broker or foodservice company that likes to boast about some of their best customers, but most are fairly protective of their customers.
There is also the matter of steps taken by pizza operators, both large and small, to inform and educate their employees about their trade secrets, the need to protect such trade secrets, and some of the penalties for breach of their obligations to maintain and preserve such trade secrets. Obviously, the biggest companies, like the major chains, do a much better and more comprehensive job on this score than small operators. The big companies use employee agreements, train their employees, do regular field audits, and have a wide variety of manuals and the like that are developed to protect their mutual interests. Small operators usually employ few if any of these safeguards, and they do not have the volume to justify proprietary flour and sauce formulations or the special packaging that goes along with such products. Also, many employees are unaware of any obligation to protect disclosure of trade secrets. In most cases, they have never been made aware of the trade secrets or any obligation to protect them. They are usually the most vulnerable to revealing such information. With Facebook and Twitter (and other social networks) and with YouTube and other video producers, and even forums such as ours, there is even a greater likelilhood of employees revealing proprietary and trade secret information. And there is not a lot that can be done to fully protect proprietary information and trade secrets in such cases. However, there are a few things that might be done, such as educating employees on the need to protect the product, not posting dough formulations and sauce and spice blends all over the workplace for everyone to see and copy, and controlling the trash of the business so as not to be accessible to dumpster divers. Assigning only certain employees to certain tasks and keeping work areas away from view of customers and non-employees may also be good measures to take.
There are also limits as to how far one can go to get a worker in the pizza field to reveal proprietary information or trade secrets, or to take other measures, such as dumpster diving. Although I have not researched the matter in detail, I understand that it is illegal in some parts of the country to dumpster dive. It may well be that any such laws are not strictly enforced, and the penalties may be minor, but it is something that one should be aware of. It is also not a good idea to try to get an employee to reveal trade secrets through bribes. That might cause the employee to lose his or her job if disclosure of legitimate trade secrets is discovered, but in some jurisdictions, bribing such an employee may be illegal. It's important to keep in mind that "trade secrets" actually have to really be trade secrets. As we all know, just about everyone in the pizza business touts their products, whether it is their pizza dough or their sauce, as being trade secrets when we all know, or have later discovered, were not.