Since the mice are on a ship for most of this book, we're guessing that the title refers to the Atlantic Ocean. After all, when the mice are at sea, they are on some crazy adventures.
But what about these secrets that the title speaks of? Well we know there are oodles of secrets on this ship—Olive keeps her engagement hidden from her parents, Helena doesn't tell her sisters about her jaunt with little Lord Sandown, and Beatrice is being pretty hush-hush about her secret boyfriends for the whole stinkin' book. Yup, we've definitely got lots of secrets.
And eventually all these secrets come out. By the end of the book, everyone knows everything. As Helena says: "There are no secrets at sea" (13.1, 14.44). Oh snap.
So on the one hand we've got lots of secrets in this book, but on the other hand we've got tons of gossip so nothing stays hidden for long. Either way, the title lets us know that there are some secrets afoot. And if we read on, we're going to find them out.