The example that springs to my mind is Abersoch in North Wales; a classic Harry Varden nine hole links course of true quality, to which has been tacked on a further nine holes on an adjacent cow pasture. I've not yet played it but I believe Portmadoc along the coast is a similar case.
Helsby in Cheshire has a very good back nine designed by Braid preceeded by a rather uninspiring front nine added later. Up the road from me I remember Marple being a nine-holer back in the 1970's and a 14 or 15 holer in the early 90's. Soon after that it was extended to a "full" 18 holes shoe-horned onto pretty much to the same piece of land!
To my mind it is a real pity that 18 holes ever became such a rigid standard for a golf course. It has led to a belief among most golfers that 9-hole courses are not to be taken seriously, and that courses with 12 or 15 holes are just plain weird! It has also led to unsatisfactory solutions such as those outlined above, not to mention the problem of a game of golf taking up pretty well the whole of a day once travelling, warming up, and a couple of beers afterwards are considered. This may not have been an issue to Edwardian gentleman golfers with dutiful wives at home attended by servants, but it most certainly is a big problem today in attracting young family men to become golf club members.
Ideally the number of holes on a course should not be a standard number; but flexible according to the land available. Handicapping would simply require a mathematical adjustment. If we had to be bequeathed a standard number of holes by our illustrious forebears I just wish they had picked on 12 or 15 instead of 18.
In the unlikely event of 12 holes suddenly becoming the standard golf course Reddish Vale would be a world class facility and we'd have a few mill in the bank from the sale of land for housing and the current clubhouse as a nursing home!