Thanks for the help, guys! I'll check the Water disturbance thread. Also, thanks for pointing out the useless 16km-Atmo in there.
My problem was the Merchant Fleet Mod. Before starting with my month old SH3, I applied the latest exe fixes by h.sie - but I forgot to tick the 4GB-Patch-Option for 64bit machines. This obviously made my game run on not enough RAM.
But may I say this: After those months it's great to see this community as helpful and friendly as it's always been!