The original purpose of TOR was to provide agents and handlers with a means of secure communication, allowing them to organize subversive or espionage activities. It was created by the Department of Defense to propagate their interests and spread democracy around the world using these secure capabilities. Given this context, it's not unreasonable to assume that TOR is still being used in a similar manner today.
Because of its origins, access to the identities of users on the TOR network—even if they could be de-anonymized—would likely be extremely restricted, compartmentalized, and classified. This would make it much more difficult for such information to be used in law enforcement proceedings. Perhaps that, rather than a technical limitation, is the reason most high-profile arrests related to TOR involve criminals making some other mistake, rather than the security of the network itself being compromised.
Additionally, it’s interesting to speculate that some of the secure private defense and intelligence networks—parallel or classified world internets—could themselves be implemented as possibly enhanced forms of TOR. It would make sense that nation-states, through shell companies and other disguises, might run and control many seemingly innocuous machines acting as secure relays in these parallel networks. While I have no data to back this up, it seems logical, given that TOR was originally created by the DoD and then open-sourced.
Why wouldn’t they keep something that works, build on it, and enhance it as a means to secure their own global communications?