I think that the reason for this is that Victor Frankenstein is just absolutely obsessed with catching up to the creature that he has created.
When Victor meets up with the ship, he is chasing the monster. He is down to a sled with just one dog and is in terrible shape. This means that he has already shown that he is completely consumed by the need to catch the monster.
So it is not too surprising that he thinks it is important to know where the ship is going. He does not want to leave without catching the creature.