Yeah, that's what doesn't make sense. The moment the Straw Hats left Zou for Whole Cake Island, Carrot swooped in like "HEY!! I'M HERE!" but now it's the complete opposite.
She doesn't have a reason to stay hidden for so long. It's not a secret, and it's not like the Straw Hats wouldn't love to have her join them.
The only thing I can think of that would clear up this situation is if she's in ones of the rooms, probably sleeping. This would make the most sense and would explain why we haven't seen her outside with the Straw Hats. I don't see how
anyone could sleep when they're literally falling down a waterfall, but it would fit with Oda's humor.
But then there's the question: Why didn't she tell them? What, she was the first to arrive on the Sunny and got tired of waiting? There's so many questions that need answers!