Maybe I'm misunderstanding but since this 3D CPU would be superconducting, it would conduct electricity without resistance and therefore not generate any heat while in use.
The adiabatic (reversible) computations themselves would be zero-loss, but in order to actually read the result of your computation you need to waste heat.
Maybe there are parts which are not superconducting? Like impurities in the material. So even though the generated heat is like 0.01% of the original, some heat is still generated.
