At some point in time, every woodworker has cursed the fact that wood expands in humid weather and contracts in dry weather. Because of it, lumber that was once straight became curved, twisted, or both. Parts that once fit snugly became loose, or impossibly tight.
Turning green (freshly cut) wood was how I learned firsthand how much wood can move, and how quickly it can move. I got hooked on turning goblets, which were fun to turn, and could be turned in an afternoon. I learned a lot about grain direction, wood’s strengths and weaknesses, and, after about a week’s time drying, how much wood could change shape as it dried.
I have added three goblets to my website that are for sale, at a price of $30 each.
As long as we are dealing with solid lumber, wood movement is inevitable. Don’t ignore it and don’t fight it. Accept it.
When designing, I take wood movement into consideration. Sometimes that means using wood cut a certain way (e.g. quartersawn) to focus the expansion and contraction in one direction. Other times, it means using reinforcement (e.g. battens) to keep things aligned. And sometimes, it means just letting the wood do whatever it wants.
If you are interested in learning more about turning goblets from green wood, I recommend Turning Green Wood by Michael O’Donnell, one of the books on my page, Recommended Readings.
Sculptural Woodwork by Chris Wong 
Yes, wood moves, and especially in a marine environment. We built a Japanese Tool Box out of bald cypress and expressly designed it to allow for wood movement. The box is used to carry groceries aboard my boat, which sails the Pamlico Sound in North Carolina. We used bald cypress because it is rot-resistant and easy to work. We used minimal glueing only in planes that would move together and relied on big cut nails and the intrinsic strength of the Japanese Tool Box design to make a box that will carry a substantial load of provisions and stand up to sliding around a truck bed, being dropped on the dock and manhandled into the cabin of the boat – quite possibly in the rain. The box has seen temperatures as low as 15 degrees farenheit and as high as 90, humidity of 20% and of 100%, and is holding up well.
On the other hand, with most houses climate-controlled year-round, we don’t worry too much about wood movement in furniture for inside. We don’t ignore it, but we don’t obsess over it either. Like you said, design for it, saw for it, build for it, accept it.
That sounds like a very practical, functional box. Joinery can be fun, as can allowing or wood movement in the design, as in your case.