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When electronic circuits produce heat, that is a sign a percentage of the current flowing through the circuit is being converted to heat energy. This would be a complication in the spacecraft design and a totally unneccessary waste of energy.
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Electronics require currents. Agreed? ok, fine then. In order to have currents not create heat, you need a super capacitor. Super capacitors in general require them to be cooled to temperatures close to the absolute zero point (atthis point, their electrical resistance gets close to 0, and therefore so does their heat producing). The process of cooling close to the absolute zero takes loads of energy and produces loads of heat in itself. In total -which is relevant for a self-contained spacecraft- it costs way more energy and generates way more heat than just have the electronics run at their "native" temperature.
therefore, electronics, perfectly installed and designed, will generate heat. Quite some heat indeed. My class A preamplifier heats my room, i'm serious about that. My PC generates loads of heat. Like Jay, I got serious burns from touching a bare, running processor. This heat is simply a result of necessary currents running through materials which will have an electrical resistance in any practical case.
We could not and cannot construct a spacecraft using super conductors only.