I think this is what the map means, the X is where the storm is, and the storm carried them south closer to krawk island, so horban made a route to krawk island instead of mystery island, also the waves mean the storm

I thought that, too. It makes a lot of sense.

I disagree about the waves, because it wouldn't be a permanent storm if it just came out of nowhere like they said. Plus it doesn't really makes sense...if that's true then who drew the map? Hoban would have to have come back on board to draw all that

 

My theory is the waves are a section of ocean that normally is very rough. He wanted to get off at the X, swim to the circle (a boat or other ship maybe), and then take it to Krawk. But hey I bet all of us end up being wrong, they keep surprising us!