In the quasi-two-dimensional (quasi-2D) copper- and iron-based superconductors, the onset of superconductivity is accompanied by a prominent peak in the magnetic spectrum at momenta close to the wave-vector of the nearby antiferromagnetic state. Such a peak is well described in terms of a spin resonance mode, i.e., a spin-1 exciton theoretically predicted for quasi-2D superconductors with a sign-changing gap. The same theories, however, indicate that such a resonance mode should be absent in a three-dimensional (3D) system with a spherical Fermi surface. This raises the question of the fate of the spin resonance mode in layered unconventional superconductors that are not strongly anisotropic, such as certain heavy-fermion compounds and potentially the newly discovered nickelate superconductor NdNiO2. Here, we use the random phase approximation to calculate the dynamical spin susceptibility of 3D superconductors with a d(x2-y2)-wave gap symmetry and corrugated cylindrical-like Fermi surfaces. By varying the out-of-plane hopping anisotropy t(z)/t, we demonstrate that the appearance of a spin resonance mode is determined by the topology of the hot lines, i.e., lines on the Fermi surface that are connected by the magnetic wave vector. For an in-plane antiferromagnetic wave vector, the hot lines undergo a topological transition from open lines to closed loops at a critical t(z)/t value. The closed hot lines cross the nodal superconducting lines, making the spin resonance mode overdamped and incoherent. In contrast, for an out-of-plane antiferromagnetic wave vector, the hot lines remain open and the spin resonance mode remains sharp. We discuss the experimental implications of our results for the out-of-plane dispersion of the spin resonance mode and, more generally, for inelastic neutron scattering experiments on unconventional superconductors.