Many in the 40s community use such a variety of keyboards that it might be hard to standardize, and also my experience is that most use blanks. I'm using mostly 40% keyboards, and since I'm using Colemak DHm mod, and not Qwerty, the question has been more prevalent.
However, I've talked to some people and come to the conclusion that,
1. Using blank keycaps is better for touch typing.
2. Leaving the caps as Qwerty is nearly as good as blanks.
3. Most people are using 60% and larger, and Qwerty, thus I'll have to accept the limited amount of options. E.g., even if they support Colemak they will probably not support DHm.
4. Sometimes there are sets that are compatible, e.g. the IC on KAM superuser, but then you will have symmetric profile which bothers some.
This being said, if you are using 40%-60% keyboards with Qwerty, then most GBs will have support for that. However, I do agree that it feels unnecessary to buy, "too many" caps. But now and then there are good GBs for your needs.
I am currently typing on blank pbts from Kbd fans on an ortho, very happy with these.
There are people that have designed what you might be looking for, check out PrimeKB, although that is designed for 40%.
