I think eventually they should.
It will cause a real problem if, for example, operations engineers try to make optimisations based on the data.
For a toy example, you could imagine someone might analyze the wait times and determine that the burger frying is on the critical path. Kitchens could be instructed to add an additional person to frying burgers while reducing the headcount at the drinks station. ( You can probably tell I haven't worked in a McDonald's kitchen, but bare with the example. )
However there is a hidden reality given the data was complete fiction, and it could be that the drinks were in reality on the critical path, and this intervention which a computer model predicts will boost throughput will actually harm it.
Of course the reality of operations research will be a lot more nuanced and subtle than that, but the conclusion that fake data will lead to expensive incorrect interventions and suboptimal optimisers stands.
There is also reputation to consider. If McDonald's gets a reputation as somewhere people avoid because they are put off by the broken system, then they should be proactively working out why.
It may well already show up in satisfaction surveys that people are put off by "the computer system", but it may be misattributed to the ordering UX rather than the complete package that includes the broken tracking system, fundamentally broken by misaligned incentives.