Vulkan 1.0.18 now resolves this issue. It now makes it perfectly clear that:
The input to blending or color attachment writes is undefined for components which do not correspond to a fragment shader output.
As such, setting the write mask to none should be fine, since the value itself is undefined, but it does exist. And since nothing will be written, there's no reason to consider the state invalid.
So definitely file this as a bug to the maintainers of the validation layer in question.
Well, this poses a problem.
On the one hand, there's no reason why that shouldn't work. Whatever the value is, you're masking it off, so it is irrelevant.
On the other hand... the Vulkan specification says nothing about what happens when your FS doesn't write to an output. It doesn't say if it's legal or illegal. It doesn't say if that output is merely undefined or if the entire pipeline yields undefined behavior.
So either the validation layer is wrong or what you're trying to do is not intended to be allowed. But until the Vulkan specification clears this up, there's no way to be sure which.