Yes, the 16 foot Old Towns generally lacked a center thwart, but the 17' and 18' models usually had a center thwart attached with wingnuts for easy removal. Unfortunately, this also meant easy loss, as you now know. If yours is an Old Town from the earlier days, it would have countersunk bolts covered with bungs as you describe. The thwart style changed at about the time that they went to diamond-head bolts. The earlier thwarts are plainer, in a sense, but I think they are much more graceful than the later ones (and then they got even less graceful later on when they were shaped with a sharp edge along the top of the thwart).
If you email me a photo of the existing thwarts, I can trace an appropriate center thwart. As Mike is C. said, the center thwart is a longer version of the quarter thwarts, but the profile shape is not identical- the profile is lengthened; otherwise, the center thwart would have the same center profile with longer square ends. This is not the case- the shaped profile is carried farther out, giving the center thwart a more graceful shape than if it had long square ends. Again, email an address and send (or post) photos and I can send you a tracing.
Michael