Matthew:
Your question is a good one.
I think the prevailing wisdom among architects would be that a nine-hole course should cost 50-65% as much as eighteen. It's half as many holes, but you still have to figure out a routing, you still have to go to a pre-bid meeting, and you're probably going to make more than half as many site visits. This is in line with the conventional wisdom about maintenance costs for nine holes being 60-65% as much as 18 holes, because you still need a superintendent and a mechanic and a lot of equipment (which just won't wear out as fast).
However, having built the nine-hole course in California just last year, I am wondering if we aren't all wrong about our assumptions. There is just so much less expectation of a nine-hole course that it doesn't have to be built at a big scale like modern 18's. We built smaller greens and narrower fairways and fewer bunkers, so the cost of construction was nowhere near half of what it will cost to build the new 18 holes nearby (if we ever get approval to do that one). And by the same logic, I don't think it will cost nearly as much to maintain -- certainly not once it shares some equipment and a mechanic and superintendent with its big brother, but I'll try to get the numbers for the short term for comparison, as I suspect they're MUCH lower than 18 holes would be.
To go back to your original question, I didn't charge nearly half my fee for that nine holes, because it was a throw-in on the larger deal ... but having done it, I think I will charge quite a bit less than half our fee for anyone else who wants to build nine. The only problem is then I'll have to cross my fingers they don't ask me to come back and build a second nine alongside it the next year!