... Musk is on record about not filing patents for SpaceX's stuff, relying on secrecy instead, his concern being that China will simply use the patents once published.
Allegedly, prior art didn't stop Makerbot from filing the patent either. But on further research, it seems that my understanding of the Makerbot situation was incorrect. (I had read one of the initial articles when the story first broke but hadn't subsequently followed up on it.)
So Patents on something with prior art will make it through, but not necessarily be enforceable. In fact it's impossible to avoid if SpaceX does something novel, and doesn't tell anyone HOW it does it, then a competitor who comes up with the same answer won't realise they're doing it the same way when they patent their method. Perhaps SpaceX will approach it like copyright.