The "clean room" part of clean-room reverse engineering implies that there is no exposure to the original copyrighted code on the part of those doing the reimplementation, whether human developers or AI. Traditionally, if you're working of the source code itself, you have one party translate the source code back into a design document, specifying behavior, and then you have another party implement that design spec with original code.
If you already have a running copy of the software to model the behavior off of, then you don't need the original source code in the first place. So going closed source will have zero effect on the capacity of AI tools to be used for clean room reverse engineering: all you need is the runtime.
> But I'd want to see more adoption of something like the Ship of Theseus license (https://github.com/tilework-tech/nori-skillsets/pull/465/cha...) before giving up on open source entirely
This license doesn't seem valid: a license can't redefine what qualifies as a derivative work. That's determined by copyright law itself, and if copyright law says that a clean-room reimplementation isn't a derivative work, then it isn't restricted by copyright, so doesn't need a license in the first place.
Since such "clean room" implementations ostensibly do not see the source, it's arguably irrelevant whether such sources are open are not. Such implementations will happen regardless of whether the sources they're reimplementing are opened or closed.
Whose theory? That makes no sense at all. The creator can spend the same amount on tokens whether it is closed or open source.