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You need to understand what counter is.
A counter to Tsukuyomi is basically immunity, such as Sasuke.
A check just avoids total damage, what Kakashi did was a check. If Kakashi was hit by Tsukuyomi again, the results would have been the same.
No because by that time Itachi's head is in Kamui world or he is coughing his life out due to trying to use Tsukuyomi again.