Cylindrical magnetic nanowires with large transversal magnetocrystalline anisotropy have been shown to sustain non-trivial magnetic configurations resulting from the interplay of spatial confinement, exchange, and anisotropies. Exploiting these peculiar 3D spin configurations and their solitonic inhomogeneities are prospected to improve magnetization switching in future spintronics, such as power-saving magnetic memory and logic applications. Here we employ holographic vector field electron tomography to reconstruct the remanent magnetic states in CoNi nanowires with 10 nm resolution in 3D, with a particular focus on domain walls between remanent states and ubiquitous real-structure effects stemming from irregular morphology and anisotropy variations. By tuning the applied magnetic field direction, both longitudinal and transverse multi-vortex states of different chiralities and peculiar 3D features such as shifted vortex cores are stabilized. The chiral domain wall between the longitudinal vortices of opposite chiralities exhibits a complex 3D shape characterized by a push out of the central vortex line and a gain in exchange and anisotropy energy. A similar complex 3D texture, including bent vortex lines, forms at the domain boundary between transverse-vortex states and longitudinal configurations. Micromagnetic simulations allow an understanding of the origin of the observed complex magnetic states.