Clarification: When I say "custom" wheelset what I really mean is "wheelset built by an independent craftsperson." That wheelset MIGHT have been built last week in his or her shop, before you were a customer, with no input from you. Or it MIGHT have been built with exactly the hubs, spokes, rims, and lacing that you asked for. But it was not a stock model from a major component brand.
In my experience typically it was blend of the two: You told the guy what you wanted and then he told you why that was a stupid idea. Then he talked you into letting him build what he thought you should have. Then you told all your friends about the custom wheels you'd had built.
This was definitely true with the curmudgeon builders like Peter White, referenced above by
@KevinF . I never got to ride on Mike Curiak wheels (also referenced above, by
@Tom K. ), even though I tried to get a pair 11 years ago for my first 29er. He didn't return any of my emails. These guys have attitude, that's for sure. I did end up with a front MTB wheel from Gravy Wheels once, and it was noticeably superb.
20 years ago I'd do a huge preseason order of rims from Mavic and build wheels all year. Now, I don't even keep rims in stock. The wheels I do build are much more expensive than what was imaginable back then. I'm building up a pair of Onyx hubs (silent BTW) with carbon rims for a customer this week.
I think what I am hearing from people is that my observation is correct: Many of the folks who, 15 years ago, would have been on custom wheels no longer are. However, I haven't learned
why not. The speculation in my head when I started the thread was, "Maybe carbon rims are so reluctant to go out of true or break that you don't need to be a master wheel builder to make a wheel that lasts and performs well. And maybe so many of the former custom-wheel buyers are on carbon rims that this explains the phenomenon." (Plenty of casual riders are obviously still on alloy rims, but when and if they replace a wheel they're probably not looking for even a mid-range item.)