For a discrete dynamical system, the prime orbit and Mertens’ orbit counting functions describe the growth of its closed orbits in a certain way. The asymptotic behaviours of these counting functions can be determined via Artin–Mazur zeta function of the system. Specifically, the existence of a non-vanishing meromorphic extension of the zeta function leads to certain asymptotic results. In this paper, we prove the asymptotic behaviours of the counting functions for a certain type of shift spaces induced by directed bouquet graphs and Dyck shifts. We call these shift spaces as the bouquet-Dyck shifts. Since their respective zeta function involves square roots of polynomials, the meromorphic extension is difficult to be obtained. To overcome this obstacle, we employ some theories on zeros of polynomials, including the well-known Eneström–Kakeya Theorem in complex analysis. Finally, the meromorphic extension will imply the desired asymptotic results.