Since (cleanly) installing 1.3 I've had this EXACT same issue.
It doesn't matter what settings you have, you could be running it at 640x480 with nothing turned on and it'd still go at around 2 fps.
It seems to have something to do with the wakes/boats.. If I look out into the empty sea, I get 100 fps.
As soon as I turn the camera around to look at one measely little warship, the game stutters so violently I have to hammer the ESC key at least 10 times before it responds (and then do battle with the laggy mouse).
NOOOOOOOOO, basically
WTF!