I'm a firm believer in keeping IC and OOC knowledge separate but also out in the open. So in a lot of ways I think that having the secrets be known out of character is the idea situation. But if you disagree with me, you may want to skip the rest of this thread. Or start another one.
Here is where I want to talk about secrets.
Secret #1. The boat itself is a former Spelljammer.
Not only is it a former Spelljammer, it's intelligent, and it's broken. It does not communicate (except perhaps sporadically, perhaps through dreams or another obscure method).. and it does not fly. The engine powering the craft is a mystery- exactly how it works, isn't clear- the gondsmen operate it, the ship's engineer Jowan seems to have mastered some level of control of it. It is likely that she will be the first character to truly understand the ship as an NPC.
Another thought I had was to do a sort of Mister Snufalupagus on the boat, where it occaisionally appears to communicate with one or two characters when nobody is around, but when a second person shows up, the communication disappears.
This fact will be completely un-knowable until the characters start to get close to Paragon level. There might even be some adventures at some point where the boat has to react to some kind of massive hazard, and the only option is to try something desperate like get it to fly or go underwater like a submarine. In a special adventure, this is exactly the kind of capability the Nixie Queen will have (and where it got it's name).
Any other ideas? Let us know! Note: you may be called on to DM or create adventures if you have good ideas!!!