Spot on. The power supply goes into self-protect mode, where it constantly attempts to seemingly restart the power flow. The "whoop" or "flup" sound (both of these sounds are correct) is the floppy disk drive attempting to start up, being cut short, attempting to start again and so forth, all in time with the power supply starting and restarting. If the FDD is disconnected, in this case the machine powered up just fine, but on machines with deeper issues you'll only hear the PSU whistling in time with where the "flup" noise would normally occur.
It's caused by one of three things, unfortunately all three are pretty broad headings and require some narrowing down to determine the direct source of the issue.
It sounds like 1 or 2 are the most likely in your case, but it requires some knowledge of the superdrive to narrow it down. Additionally knowing which component let out the smoke would also be a handy hint. I can only deal with issues 2 and 3 for the most part, but everyone here already has it covered.