yes, there are a bunch of ninjas who counter 6p, most of them behind a paywall, the only one which I don't see so often is f2p Gengetsu, but very hard to get his brakes.

Kakuzu is like sugar - you can put him on any team and it works, i guess that's why many people feel he brakes the game but he came as a cheaper counter to Kabuto sage, so somehow he makes sense, strangely Kabuto even with the brakes didn't become so widely used.