A lot of magazine articles have stated the '61 '09s were all in the Super Sports, so many people believe that. The SS option didn't appear until Feb. but the first '09s showed up in Dec.(1960). They could be ordered in any full-sized body style.
It's probably near-impossible to tell if a restored '61 was originally an '09 without paperwork - unless some mistakes were made. And there aren't many clues on an un-restored body either.
As far as the engine itself, another UN-proven rumor is that some 2x4 cars were built near the end of production. Several of the top name racers back then showed up in July with 2x4s and the big heads, but they were put into OS/S (Optional SuperStock), which was the predecessor of FX. Those parts were supplied over the counter. All production '61 409s seem to have had a single AFB and were rated 360hp.
Hope this helps.
Verne