This morning Supercell clarified what’s going on with their recent policies to encourage “fair play." According to them, accounts that were found using 3rd party hacks and cheats were banned for two weeks this time. Per Supercell, “When those 2-weeks are up, any accounts continuing to utilize 3rd party software will be permanently banned. Bans are non-negotiable." So, if you at all care about keeping your Clash of Clans (Free) account, consider this your one warning to uninstall all your third party utilities.
— Xmodgames (@xmodgames) April 26, 2016
Amusingly enough, the guys behind Xmod (the largest Clash of Clans third party cheat) have taken this as a challenge, and per the above tweet are going to be improving their anti-detection algorithms. These sort of things are always a cat and mouse game in basically every online game I can think of. The developers will figure out how people are cheating, ban a ton of players, hackers figure out how developers were detecting them, update their cheats, and the whole process repeats itself.
But, for the time being, it seems like a good idea to not cheat in Clash of Clans.