I run the game under Linux (using Wine) and I too get lag at times in the Nav map, though I have 4Gb of RAM and 4 cores in this machine. I think it is caused by the game loading data from disk (ship skins, smoke, etc.). This is where lots of RAM helps, because more stuff can be loaded in RAM so the disk won't be accessed as much. Linux, arguably more memory-efficient than Windows, still suffers these slow-downs so I don't know how much can be done about it, apart from low-texture skins, few mods, etc.
That being said, I rarely raise TC above 128x, and then it is almost non-noticable on my set-up. I may see the boat freeze for a second or so, and then everything is smooth again.
And as Osmium Steele mentioned...when you notice the lag, better to do sound check. Something's around!
