Are you telling me he knows exactly what of the hundreds of settings used on their simulator would be day to day, and would have suspicions about where those settings came from? Don't you think that would be down to the simulator engineers and performance analysts? Do you think McLaren is run like some kind of KGB outfit with everyone monitoring everyone else and all reporting to Ron?
If the FBI and the CIA get caught out by spies working in their own organisations for years on end, how do you expect the head of one company to keep track of everything a dishonest employee is doing? Even companies that log every single little thing down to the keypress don't double check everything that's ever happened until something goes wrong. It's simply not possible unless you have a whole second company to double check the first one. Even banks or security services, where exactly this kind of environment exists, get caught out by the dishonest employee who has learned the system and is deliberately trying to circumvent it.
It's also not the bosses job. They are supposed to govern how the whole company runs, and set up the framework for how the people beneath them do their jobs. They are not supposed to be checking over everything an employee does every day. You employed them in a job because you thought they could do the job without you having to watch over everything they do. Otherwise you might as well do it yourself. You don't know an employee has no integrity or honesty until they exhibit that.
Fact is, F1 is a small and rarified sport. People mix socially and information moves around. Staff moves from one team to another and takes skills, expertise and knowledge with them. Spying on your opponents and what they are doing has been accepted by the FIA for years on a "don't ask, don't tell" basis. Rules are bent as far as they can be, and sometimes more so.
Mclaren has a set of rules governing the behaviour of it's staff. Coughlan, DeLaRosa and Alonso broke those rules, and the system inside McLaren didn't catch them. It assumed them to be honourable and honest people until (as has been proved) they showed that they were not.
You could argue that the system did finally catch the cheats when Dennis found out and told Mosely, that the system only did work once Dennis was in the loop at that low a level. Dennis was not expecting it to be true because Alonso recanted his threats to Dennis, but it turned out that Alonso was lying about that too. The only way for Dennis to know about what was going on was the emails (which Alonso had hidden and only brought out to blackmail Dennis), and the mobile phone call records, which no one had access to until the Italian Police produced them as part of the ongoing sabotage investigation into Stepney.