Yeah, there's a ferry from Rostock to Helsinki. However I'm trying to reduce my travel-related emissions, and after crunching the numbers have concluded that the best option would be ferry+train via Sweden, with electric car via Sweden a close second (per head, assuming two people or more in the car). Fingers crossed for that tunnel and a direct overnight train connection!
My understanding is that these numbers (try to) account for actual real world usage rates. Actual emissions will of course depend on a whole lot of things, including the things you mentioned, prevailing winds, etc. Same for estimating grid emissions for charging the car of course - the exact mix of sources is always in flux.