I was wrong, the bytes of the output are still swapped in the S7-1200 ( thought they have changed the endianess compared to the S7-300).
If your counter is of type integer, and you write the CV to QW0, then Q1.0 is set when CV = 1, Q1.1 when CV = 2 and so on.
If you need to set Q0.0 when CV = 1, then you have to swap the bytes of the CV value.