This makes perfect sense if the Superdrive is pulling more power than the 400K drive.
Also, I have seen an analogue board smoke before without killing the Mac. In fact, I have seen an analogue board smoke without finding any obvious scorching or burn marks. However, one thing is certain. If your analogue board is out of adjustment enough to cause smoke, then you have yourself a ticking time bomb and it is only a matter of time until merely flipping the power switch with only the stock hardware blows it up.
You have far bigger problems right now than whether the floppy drive works. And the Superdrive had nothing to do with it. Your Mac's analogue board is on its last legs and in dire need of repair. The longer you wait the worse the cascade of damage.