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I don't have a great answer for you why, but heat must be radiated away from space ships faster than you might think. They have heaters on them to keep them warm. Think Apollo 13 when they turn off all their power, and it gets cold.
The ISS is traveling through a decent amount of atmosphere still, hence they need to boost their orbit occasionally. That atmosphere is probably plenty to dissipate WAY more heat than sound creates.
That doesn't explain deep space ships... But they do clearly radiate heat, if not slowly. But probably faster than what little heat sound creates. (Also think of the cooling phase that James Webb space telescope went through)