I had this bug occur to me 3 times (the thrid instance is futher down the post: http://imgur.com/a/gKwXU
Whenever Walani goes into the fog and comes out the other side, until she either leaves her boat by hopping to another boat and back or on land and back the boat inventory is completely hidden. I had this happen to me with default world settings and my Armoured boat had a cloth sail and a Boat Torch on it. I don't know if this is a one off thing (Only my world or something along those line) and I do understand that this is early access gameplay but it is a major pain in the ass as shown in this image as I couldn't turn off my Boat Torch (I haven't ever gotten a boat lantern and have no experience trying dev console but feel free to try it out yourself)
That is all, it may be a mod related glitch but I'm only running Geometric Placement,Combined Status,Smart Crockpot,Minimap HUD and all of those mods have no effect on boats or their inventory.
Play Walani and go through the fog in an armoured boat (I haven't done extensive testing) with a cloth sail and boat torch. It may have also had something to do with the time cycle when I went through the fog as it wasn't 100% of the time but I believe it happened when I'd go into the fog near the end of a day and it would change to evening or night (Same happened with evening to night)