Ships are slow in real life. Last time I used the ferry from Saßnitz (Germany) to Trelleborg (Sweden) -- about 120 km across the Baltic sea -- a one-way trip took a bit more than four hours, I think, so traveling speed is about 30 km/h. That's ridiculously slow, compared to the time a train would need for the same distance. However, the ferries used to carry not one, but several trains at once in the past, plus cars and trucks! So you exchange speed for volume. If you feel ships are too slow, just build a couple more of them and put them on the same route. That way, you could have one ship being loaded at Port A, another being unloaded at Port B, and one or two traveling from A to B and/or B to A at the same time.