I think I am able to prove the following result which gives a partial answer to my question.
Theorem:
Let $n \ge 3$ and $d > n/2$. Then $\alpha_n^d$ (the number of zero-sum free $d$-tuples in $\mathbb{Z}_{n}$) is given by
$$\alpha_n^d = \phi(n) {n-1 \choose d},$$ where $\phi$ is the Euler's $\phi$-function.
Proof. To count these zero-sum free $d$-tuples, it is enough to count the number of minimal zero-sum $d+1$-tuples in $\mathbb{Z}_n^{d+1}$, where a minimal zero-sum $d+1$-tuple is a vector in $\mathbb{Z}_n^{d+1}$ whose sum of components is zero but no proper nonempty subset of components adds up to zero. It is an easy exercise to show that these two collections have the same cardinality. We now use the following characterization of minimal zero sum sequences (unordered) in the range $d > n/2$ given in [1].
Theorem[1]
Every minimal zero sum sequence $\alpha$ of length $d > n/2$ in $\mathbb{Z}_{n}$ for $n \ge 3$ is of the form $x_{1}g, x_{2}g, \dots, x_{d}g$, where $g$ is a term of $\alpha$ which generates $\mathbb{Z}_{n}$ and $x_{1}, x_{2}, \cdots, x_{d}$ are positive integers whose sum is $n$.
Consider the natural action of $Aut(\mathbb{Z}_n)$ on the minimal zero-sum $d+1$-tuples. When $d > n/2$ it can be shown using the above theorem that this action is free and hence each orbit will have size $|Aut(\mathbb{Z}_n)| = \phi(n)$. Moreover, each orbit $O$ is of the form $$O = \{ g (x_{1}, x_{2}, \cdots, x_{d+1} )\, | \, g \text{ is a generator of } \mathbb{Z}_n \}$$
where $(x_1, x_2, \cdots ,x_{d+1})$ is an ordered partition of $n$ into $d+1$ positive integers. This tells us that the number of orbits is equal to the number of partitions of $n$ into $d+1$ positive integers. The latter can be shown to be equal to ${n-1 \choose d}$. Thus the total number of minimal zero sum $d+1$ tuples is $\phi(n) {n-1 \choose d}$. By the remark at the beginning of the proof, this number is also equal to $\alpha_n^d$.
References
[1] Savchev, Svetoslav; Chen, Fang
Long zero-free sequences in finite cyclic groups.
Discrete Math. 307 (2007), no. 22, 2671–2679.