$d=n-s$ is called the decrement of the permutation $\sigma$. It not always is equal to the minimal number of transpositions needed to write $\sigma$.
Example. Assume for simplicity $n=2$, i.e., we are in $S_2$. The identity permutation $e=(1)(2)$ is of degree $n=2$, and it has $2$ disjoint cycles. Hence its decrement is $d=2-2=0$. But $e$ cannot be written by zero transpositions.
By definition a transposition is a permutation of type $(ij)$, and hence we have to write, say, $e=(12)(12)$. At least two transpositions are needed. You cannot write, say, $e=e$ and call it transpositions decomposition by zero transpositions because $e$ is not a transposition.
By the way, for this very same reason we in the Fundamental theorem of arithmetic require that the integer $n$ must be greater than $1$ to have a decomposition as a product of primes. For, the equality $1=1$ cannot be interpreted as a product of zero primes.
My students had seen this page and discussed the issue with me. Hence I add this remark here.