Swamped

It occurs to you suddenly that the cook's face doesn't stand out much. You mainly recognized him by the very distinctive outfit.

So what if someone - maybe Lou, maybe someone else - was dressed up as the cook, and Colleen noticed?

That also might explain why they're serving stew. A fake cook might not know enough to make something more elaborate. Or how long onions should be boiled, for that matter.

It doesn't answer all your questions, but quite a few of the oddities are explained by it. Get the cook out of the way, send an impostor, and use the kitchen as cover for the printing press. The second mate's probably involved in order to help cover things up.

But when it comes down to it, all you have right now is a guess. Maybe a few more questions to Colleen can help you get a sense of how close it is.