I don't think you'd see a thing go through the club's accounts. If you were going to do this, it would be via a sponsor or other backer of the club, and they would make the payment to the player in lieu of an inflow to the club.
The money would have to leave the Club though. If the NRL had oversight of all Clubs accounts they would be able to see that a payment was made to an organisation and be able to question what the payment was for.
At the present time the NRL has little control over the Clubs and essentially the Clubs agree to be part of the NRL. Until the NRL changes the set up where the Clubs are controlled by the NRL it makes it harder.
You could also have harsher penalties, like revoking NRL licences if you're serious.
If the NRL was responsible for paying all players centrally it would also limit the ability to rort the Cap. The Clubs could just say we want this guy to be paid this much and the NRL just pays the player that much. As the NRL grant essentially covers more than the Salary Cap, you could think they could just change the funding to the Clubs for this to actually work.
The NRL could demand ongoing access to players bank accounts.
If the NRL wanted to police the salary cap stringently it could. My guess it that it doesn't want to police it that stringently
