It's wise to be suspicious of most uses of WITHOUT-INTERRUPTS; there may be exceptions, but WITHOUT-INTERRUPTS is often used as shorthand for WITH-APPROPRIATE-LOCKING. Determining what type of locking is appropriate and writing the code to implement it is likely to be straightforward and simple most of the time.

I've only seen one case where a process's "run reasons" were used to communicate information as well as to control execution; I don't think that this is a common idiom, but may be mistaken about that.

It's certainly possible that programs written for cooperatively scheduled lisps that have run reliably for a long time have done so by accident: resource-contention issues tend to be timing-sensitive, and decoupling thread scheduling from lisp program execution affects timing. I know that there is or was code in both Clozure CL and commercial MCL that was written under the explicit assumption that certain sequences of open-coded operations were uninterruptable; it's certainly possible that the same assumptions have been made (explicitly or otherwise) by application developers.