Right, that is certainly a concern. But to play devil's advocate, it's less of a concern on the Finland/Estonia itinerary simply because the overnight ferry from Stockholm to Helsinki is part of the allure itself. I've heard the views of the Stockholm archipelago are stunning, and the food on these ships is supposed to be quite good.
I understand where you're coming from, however, which is why I'm asking this question in the first place. I do worry about cramming too much into too little time.