Colour centres are a promising quantum information platform, but coherence degradation after integration in nanostructures has hindered scalability. Here, the authors show that waveguide-integrated V-Si centres in SiC maintain spin-optical coherences, enabling nuclear high-fidelity spin qubit operations. Optically addressable spin defects in silicon carbide (SiC) are an emerging platform for quantum information processing compatible with nanofabrication processes and device control used by the semiconductor industry. System scalability towards large-scale quantum networks demands integration into nanophotonic structures with efficient spin-photon interfaces. However, degradation of the spin-optical coherence after integration in nanophotonic structures has hindered the potential of most colour centre platforms. Here, we demonstrate the implantation of silicon vacancy centres (V-Si) in SiC without deterioration of their intrinsic spin-optical properties. In particular, we show nearly lifetime-limited photon emission and high spin-coherence times for single defects implanted in bulk as well as in nanophotonic waveguides created by reactive ion etching. Furthermore, we take advantage of the high spin-optical coherences of V-Si centres in waveguides to demonstrate controlled operations on nearby nuclear spin qubits, which is a crucial step towards fault-tolerant quantum information distribution based on cavity quantum electrodynamics.