Hello there!
Ok,so the first problem.Well that's not actually a "problem" I think.It is probably related to the atmosphere mod.That ****ty water you see -it is a "low-poly" representation of water that is displayed after long ranges to reduce lag.However,it shouldn't really be that close to the camera...maybe it's a bug in the atmosphere mod?(i use the standart 8km one and I don't have the problem)
About the second problem,well,I can't really see what's wrong on the ship's hull,but that "Flickering" you get near land is probably because of the crap "colision" mapping between water and land.I get it too and weirdly enough i got something smiliar in IL-2(another great Ubisoft game).It's probably engine-related so you shouldn't worry about that.Hope this helps!
Edit: kiwi_2005 It's impossible that this is a PC problem.My PC is only slightly better than yours (I have AMD 2500+XP also called Barthon I think ,but it runs at almost 2ghz so it get's really hot but the extra power is welcome
-1 gig DDR and 6600GT and I don't really get the problem.