Personally I've never been faced with a clan that has used some type of modifications to gain an advantage, but it seems to me that a possible solution to the problem would be to have the ability to set up some type of multiple trap location options. Now this is just a idea that I thought of that could work. I'm not a programmer so I don't actually know how if they could make this happen.
The idea is this. When designing a clan war base, the traps, bombs and hidden teslas have a multiple location option. So you would designate the primary location and a secondary location for all the items that an attacker normally doesn't see.
So for this to work you would only be able to hit the attack button on the base twice maximum. So lets say you're scouting a base and you hit the attack and canceled before the 30 seconds. The next time you hit attack would be the last time you can hit attack on that base. Obviously, it would provide some sort of warning that its the last time you can hit the attack button.
The first time you hit attack the bombs and traps are in the primary location. The second time you hit the bombs and traps are in the secondary location.
So what's the purpose.
Lets say someone is using some third party software to simulate an attack and get some practice in. When they do the actual attack the bombs and traps would be in the secondary location. Then you would no longer see people dropping single troops exactly on Giant bomb locations.
If a second person attacks the same base, the traps would be in the same location as the first attacker. However, if the second person hits the attack button again the traps would go back to the primary location.
Obviously this idea has some kinks in it which i haven't figured out yet. Its just one of many possible solutions.