There are no goody huts? I'll have to fix that. I don't understand your concern about the empty ocean space. I am not sure why there are not too many natives. Every time you load the game it is different. The amount of natives seem to change.
Neither goody huts nor natives in the west/north (they are covering the south of America and Caribbean isles). Pretty strange the empty space. I will try to show you a screen-shot.
As I said, goody huts need to be added "by hand". That's a pity.
What I said about Europe tiles is simple, trade units are able to seal to Europe but pirate units will not do it. Since trade units will automatically seal to Europe when entering in the first Europe Tile available and Pirate units don't, that enormous amount of Europe tiles could lead to Pirate units to be there moving and moving without doing nothing useful. Have in mind that trade units will never go so far... so there is no reason for pirate units to allow them so.