Well having worked as a developer for a long time there are numerous ways they could go about it. Their priority should be securing the client side battles... they could also do some research on the tools that are being used to accomplish cheating in conjunction and see where they can tighten their own code up. They may possibly be able to decompile any of these tools though I would suspect they already know exactly how things are being manipulated and why.
It may be that the easiest way to clean it up would be to send communication back to the servers during battles. They know the rules of their game and what would be outside the bounds of possibility or suspicious. This may not catch smart cheaters though which is why securing their own client code might be more important in catching all cheats. They could have the server drive attacks if they wanted to. It might be more network overhead but is it worth it to clean cheating up in the game? With any server communication this obviously means airplane mode might take a hit... but why not give a message to the player at the end of battles to ask if they want to forfeit or confirm the end of the battle? Players have been using airplane mode for years to get around a constraint of the system that CG obviously deem fair play so why not just let the player confirm at the end of the battle?
The bottom line is that they can clean cheating up if they really had an interest.
