Yeah, it's a difficult one to balance. If it were me, I'd take the single fan 1650 S, as you've said it's more powerful. The noise and heat doesn't bother me.
If you case has some internal fans, and they are set up correctly, you will hardly notice a rise in case temps with the single fan GPU. Obviously both these GPU's are really for 1080p, so the extra power in the Super might translates to a better game experience.
More fans generally means a larger/longer cooler. A single fan generally means a mITX version, short cooler. While both will perform the same, the single fan is usually at a slight disadvantage thermally, so that can and will affect boost levels which can affect overall fps/details outputs.
That's assuming aftermarket Ariel fans, and the single fan not being blower style.
Single fan. Only because the two fan silence and tell advantage is not worth the performance tradeoff which is huge. It's like asking Strix 1070 vs FE 1080. I'd pick 1080. Noisy as all hell, but still much more fps. Yours wouldn't even be close to as noisy as blower cards