Counter Automata
I was a co-author for a paper where we investigated this problem for counter automata. We were able to show that the length of a shortest string accepted by an $n$-state (non-empty) counter automaton is at most $\Theta(n^2)$. See here: https://lmcs.episciences.org/5251
The lower bound can be obtained similar to how you described in your question with cycles of length $p$ and $q$ (or any two relatively prime numbers).
Pushdown Automata
Upper Bound: We can get an upper bound using standard techniques. The length of a shortest string accepted by an $n$-state (non-empty) pushdown automaton is at most $2^{O(n^2)}$.
Essentially, we argue that if the pushdown automaton's language is non-empty, then there exists some string that it accepts where the stack height is at most $O(n^2)$. Therefore, there are at most $n \cdot 2^{O(n^2)}$ (which is still $2^{O(n^2)}$) possible configurations so there must be an accepted string of length at most $2^{O(n^2)}$.
Lower Bound: For an exponential lower bound, see Jeffrey's answer above.
Also, see my answer to this related question: Shortest string in the intersection of a context-free language and a regular language
This related answer leads to a deterministic binary stack (non-empty) PDA with an exponential lower bound for the length of a shortest accepted string. Note that the construction relies on the fact that logspace bounded auxiliary pushdown automata can run for exponential time.
For example, such a machine could iterate through the numbers from $0$ to $2^n - 1$ in binary on the stack using only $O(\log(n))$ auxiliary space.
Update: A Tight Bound
Due to results from [1] (Theorems 3.19 and 4.22), it follows that there is a tight bound. That is, the length of a shortest string accepted by an $n$-state (non-empty) pushdown automaton is at most $2^{\Theta\left(\frac{n^2}{\log(n)}\right)}$. This assumes a restriction on the PDA's such that the stack alphabet is fixed and the stack pushes or pops only one symbol at a time.
After looking through the proofs of Theorems 3.19 and 4.22, as far as I can tell, this result should hold for both deterministic and non-deterministic PDA's.
Note: I find their proofs difficult to fully verify / reconstruct. Does anyone know of a simplified argument? If not, I would always be interested in looking through this further with others.
How To Apply Results From [1]
Rational Index: The rational index of a language $L$ is a function $r$ such that for every $n$, $r(n)$ is the maximum length of a shortest string in $L \cap L(A)$ over all $n$-state non-deterministic finite automata $A$. In other words, $r(n) := max_{A}\{ \; min_{x}\{ \; \vert x \vert \; : \; x \in L \cap L(A) \; \} \; \}$ where $A$ is an $n$-state NFA and $x$ is a finite string. A definition for rational index can also be found in [2].
Lower Bound: By Theorem 3.19 from [1], we get an $2^{\Omega\left(\frac{n^2}{\log(n)}\right)}$ lower bound. This is because there is some fixed context-free language $L$ whose rational index is $2^{\Omega\left(\frac{n^2}{\log(n)}\right)}$.
Let me explain. Let $P$ denote a PDA that recognizes $L$. By the preceding, there is an infinite family $\{ A_n \}_{n \in \mathbb{N}}$ of finite automata such that for all $n$, $A_n$ has $n$ states and asymptotically a shortest string accepted by the Cartesian product of $A_n$ with $P$ has length $2^{\Omega\left(\frac{n^2}{\log(n)}\right)}$.
It looks to me that, each finite automaton $A_n$ from their construction is deterministic. Also, the PDA $P$ is deterministic with a fixed stack alphabet that only pushes or pops one symbol at a time. Therefore, the lower bound applies to deterministic PDA's with a fixed stack alphabet that only push or pop one symbol at a time.
Upper Bound: By Theorem 4.22 from [1], we get an $2^{O\left(\frac{n^2}{\log(n)}\right)}$ upper bound. This is because any given context-free language has rational index $2^{O\left(\frac{n^2}{\log(n)}\right)}$.
Let me explain. Given any $n$-state PDA $P$ over a fixed alphabet that only pushes or pops one symbol at a time, we can convert it into an associated $O(n)$-state visibly pushdown automaton $P^{\prime}$ over a larger alphabet that must read a push-$c$ symbol in order to push $c$ onto the stack and a pop-$c$ symbol in order to pop $c$ off of the stack for each stack symbol $c$. The PDA's $P$ and $P^{\prime}$ have shortest accepted strings of similar length.
We can now view $P^{\prime}$ as the Cartesian product of a fixed PDA and an $O(n)$-state finite automaton. The fixed PDA's language has rational index $2^{O\left(\frac{n^2}{\log(n)}\right)}$ meaning that a shortest string accepted by $P^{\prime}$ has length at most $2^{O\left(\frac{n^2}{\log(n)}\right)}$. Therefore, a shortest string accepted by $P$ has length at most $2^{O\left(\frac{n^2}{\log(n)}\right)}$.
References
[1] Pierre, Laurent, Rational indexes of generators of the cone of context-free languages, Theor. Comput. Sci. 95, No. 2, 279-305 (1992). ZBL0745.68068.
[2] Deleage, Jean-Luc; Pierre, Laurent, The rational index of the Dyck language (D_ 1^{’*}), Theor. Comput. Sci. 47, 335-343 (1986). ZBL0632.68072.