If you want to throw a wrinkle into the question...what do you do with Montclair Golf Club in NJ which has 36 holes that it describes as 4 nines (not two 18's)? I am not asking this to be "cute" but rather to suggest a solution to the 27 holes facility question. How about saying that Montclair has two 18's with one being the routing the USGA used for the biggest event Montclair GC ever hosted...the 1985 US Amateur which used nines 2 and 4 (and calling the other 18 holer nines 1 and 3...which was the second 18 used for qualifying). I should note that the 1973 US Women's Am was played on nines 3 and 4, but the US Am history should override that).
Extending that to 27 hole facilities...I would suggest that a facility has one 18 and one 9 (instead of 3 nines) when it is managed that way (e.g. Morfontaine, St George's Hill, and The Country Club) and/or when its 18 holes course is regularly posted as a Top 100 (World or in country/region such as USA, GB&I, or Continental Europe). That way all 27 holes are eligible for a top 100 list...either 18 or 9.