High resolution scanning Hall probe microscopy has been used to directly visualise the superconducting vortex behaviour in hybrid structures consisting of a square array of micrometer-sized Py ferromagnetic disks covered by a superconducting Nb thin film. At remanence the disks exist in almost fully flux-closed magnetic vortex states, but the observed cloverleaf-like stray fields indicate the presence of weak in-plane anisotropy. Micromagnetic simulations suggest that the most likely origin is an unintentional shape anisotropy. We have studied the pinning of added free superconducting vortices as a function of the magnetisation state of the disks, and identified a range of different phenomena arising from competing energy contributions. We have also observed clear differences in the pinning landscape when the superconductor and the ferromagnet are electron- ically coupled or insulated by a thin dielectric layer, with an indication of non-trivial vortex-vortex interactions. We demonstrate a complete reconfiguration of the vortex pinning potential when the magnetisation of the disks evolves from the vortex-like state to an onion-like one under an in-plane magnetic field. Our results are in good qualitative agreement with theoretical predictions and could form the basis of novel superconducting devices based on reconfigurable vortex pinning sites.