Is there anything physically on a Super Beetle, such as the VIN, that would indicate it was manufactured at Emden or Wolfsburg?
No, not that I know of. In fact, the VIN doesn't even give away if a bug is a standard or Super until the 1973 model year.
The Wolfsburg plant stopped Beetle/Super Beetle production in June 1974. The Emden plant stopped production in January 1978. (Of course, the Super Beetle sedan's production stopped in 1975.) The Hannover plant may have had some Beetle production as details are sketchy. The same is possible for the Ingolstadt factory. The latter did build Beetles starting in 1969 when Volkswagen took over the plant. Beetle production actually outnumbered Audi production that year. I never read any details how long Beetle production lasted there so Super Beetle production there is unknown as well.
If any Supers were ever built at Hannover or Ingolstadt, they probably were not destined for the United States.
Brussels (Belgium) also built Beetles and Super Beetles. One notable special edition that was built there was the "1303/Big" (also known as the Big Beetle and the Big Bug). No Brussels-built bug ever made it to the states either unless they were imported many years later by its owner.
There were Supers that were assembled elsewhere in the world. Typically, they arrived to that country as a CKD (completely knocked down) kit. The kits were then assembled there often using local material like paint and upholstery.
Anyone know when production began at Emden?
Anyone tour Emden or Wolfsburg during Beetle production? If so, would you have any photos? Were both factories roughly the same in size and capacity?
I haven't but I would love to some day.
Did the Beetle and Super Beetle have separate production lines?
I want to say NO, they were built side-by-side, but the truth is I cannot find proper evidence of this. Therefore, my answer is I don't know.
Beetles for export (to the USA) and domestic production were built on the same assembly line. The Karmann factory assembled the last of the Super Beetle convertibles and the first of the Golf (Rabbit) Cabriolets together. Therefore, I might just be remembering these and assuming Supers and standards were also manufactured together. Another clue is getting back to the VIN in that Supers and standards shared the 111- and 112- VIN's their first two years. It would seem unlikely production would cease for one to allow for the other, or a factory would be partitioned off in some way. Whatever, I don't have concrete evidence either way.