I feel the game needs more stealth options. Two ideas:
Large foggy areas appearing at different times of a day or weekly (in game days & weeks), covering large portions of the map (say, 1/4 or 1/3 of map).
Fog would nicely provide much needed cover for stealth travel. You could offset this with lower wind conditions. If waters are calm, which they should be during such conditions, ship movement could also be provided by strong water currents that propel ships in a given direction without the need for wind in ones sails. We could "see" the currents in the same way we "see" wind direction. The helm could be used to navigate using water currents like a "jet stream".
Another way to incorporate more ship stealth might be some sort of magic talisman or spell/curse, that can render your ship invisible for a brief period of time.
Like a cloaking device of sorts, a player finds the magic item and activates it in an emergency, or at an opportune time, giving his ship complete invisibility for a number of minutes, providing the potential for escape or stealth attack, or just cover to get something done. Of course, the ship should only be invisible, but still be capable of taking damage from any cannonball, and can still be boarded. So the ship still has structure and form - it just cannot be seen. Spyglass also cannot see the ship.
If the invisible ship is flying the Reaper's flag, it should only be seen on the map. In all other ways, a cloaked/invisible ship should be able to manouever and attack/defend as usual. It can even dock invisibly at an outpost so as to unload cargo without being spotted. Once pirates disembark a cloaked ship, or jump off a ship, they should become visible. Alliances would work as usual.