Matt:
Good question. I think Steve is on to something here. Particularly in Scotland, it seems every little community has a golf course, and it seems the folks who designed and built them simply took the land that was available, and fashioned what they could out of it. Stonehaven, Cullen, Shiskine at Blackwaterfoot, Glencruitten, and Dunaverty all have tons of quirk, but little of it appears outwardly deliberate. Rather, the course was routed around the land available, and took advantage of the land forms and features available to create lots of quirk (blind uphill par 3s, a true Dell hole at Cullen, numerous blind drives and even approaches, odd-length holes, hidden punchbowl greens). In short, it'd be hard to duplicate the quirk of Shiskine, for instance, at a site like Stonehaven. Both courses are uniquely quirky in their own way because of their sites.
The truly quirky holes I've played over here in the U.S. that don't appear manufactured are almost always on older courses, such as the well-known (in these parts) 2nd hole at Eagle Springs in semi-suburban Milwaukee, which uses a glacial landform to create a novel, volcano-like par 3.