you can union boole the whole geometry and identify sharp edges with the group sop to bevel it. And if the spheres` topology does not line up with the pipes you can still melt everything together using VDBs.
NURBS would be ideal: NURBS SOPs like Project > Trim > Bridge should give you a mathematically perfect model. Unfortunately the trim node keeps crashing on recent Houdini versions when set to process profiles individually.
Rhino is a dedicated NURBS modeling program therefore it's NURBS toolset is bigger and more reliable. But for this simple object I dont think it's necessary.