Some cities can be near impossible to take if the scripter knows what they are doing. There are so many different ways for botters to protect their cities, that I would not be able to anywhere near make such a guide. If other forum-goers have input on this, and enough people contribute to such an under-taking, I would be happy to do so.
However, no matter how good a scripter is, you can always time waves to hit and take resources at the same time, so eventually, you'd be able to take down a city, whether that is killing the troops, or taking the resources. However, this would require more brute force than anything. If you compare a botted war city, and a non botted war city though, it's much the same thing. Yes, skill is involved, but generally, you'll still need to outnumber the defender dramatically.