I see your point about the buoyancy regulation but I think the author does a good job not to state too much. He doesn't really say that nautiluses change their buoyancy to move up and down. He could have added a sentence or two in their stating that nautiluses maintain neutral buoyancy through chamber regulation.... But for a NY Times article I am content with his wording.
I am a little confused about your last sentence, about indications being more positive than negative? Regarding the existence of the nautilus pearl, it is clear to me from my field research in August that many of the supposed nautilus pearls are indeed fake and do not come from nautilus. At this point, I disagree that confirming or refuting the existence of nautilus pearls makes no difference. With so much pressure already being placed on the populations, if a paper were to come out clearly stating the existence of nautilus pearls then that could mean a whole new pressure on the nautilus populations. I agree that the idea of nautilus pearls is very intriguing and would be very interesting to look at from a scientific point of view, but the ramifications that a paper like that could bring could be devastating.
Greg