Abstract The optimization of the magnetic energy of nanowires assembly is a delicate balance between the magnetic properties of each nanowire, their organization and their density inside the bulk assembly. As a matter of fact, from the simulation point of view, a dense packed structure of Co nanowires with high magnetocrystalline anisotropy and perfect alignment is the best solution to obtain a high magnetic energy and thus a powerful rare earth free permanent magnet. However, experiments have been shown that this is not a trivial task since the misalignment of nanowires inexorably occurs and likely reduces (more than expected) the magnetic properties of the final nanostructured assembly. Experiments also suggest that when the hardness and/or relative density (%) of the ensemble increases, the magnetic properties decreases casting the seeds of doubt on the realistic possibility of using these sintered materials in a new rare earth technology. Inside this frame, we report here the effect of a realistic misalignment reproducing the one observed experimentally inside the nanowires assembly. We show how, dipolar interactions and macroscopic shape contribute in different ways to destroy the magnetic energy of the bulk nanostructured material. However, we report the critical percentage of misalignment and disorder still affordable to keep the magnetic properties of the bulk material. We also demonstrate that these nanostructured materials can be interesting for their high macroscopic magnetic anisotropy. Last but not least, we show that the macroscopic shape of the nanowires assemblies presents very different critical sensibility to the misalignment/disorder of the arrangement. In particular, we report how a bi-dimensional arrangement of nanowires can be more magnetically stable compared to the tri-dimensional one. All these results give insights on the future strategies to optimize the magnetic properties of cobalt-based nanostructured material.