This could be implemented as “back 9’s” – as many people consider Kaho and Kaho Backwoods to be the front and back 9’s (respectively) of a single course.
Or, 9 holes could be added to each existing course. There could be an option to play the front, back, or all 18 when playing Challenge the Valley. (courses would go to 6 stars)
I think an easier idea to implement into would be short/long tees and/or A/B pins. The Frozen Valley lighthouse holes (and others) implement the A/B pin idea already, so I feel like it would be fairly simple to throw in a little extra code to give more options for tee locations.
Newer players can have access to the short tees first to get a feel for the terrain on a course, then once they meet a score goal (or level or PT rating), they unlock the long tees.
This would also easily allow the addition of 18-hole layouts without having to create brand new maps from scratch. You can choose to play 9 holes from the short tees, then play 9 from the longs.