Howitzers are built to fire at an upward angle -- perhaps less accurate overall when going up against a target where both the gun platform and the enemy are moving? The bazooka, on the other hand, fired at a flat trajectory.
To fire a howitzer you need to calculate the angle at which you need to fire and amount of propellant. It seems like an incredibly hard thing to do on a ship and with the enemy maneuvering. It's likely you could only guess and hope for the best.
Usually howitzers fire, observe where the shell lands and then adapt. Here this couldn't work as ships changed positions.
In other words, you are right. Having something that you can point and shoot is easier to do. This might not be true if they could aim their howitzer low but then you get the fact that howitzer cannot be steadied (it will roll with the ship) while a human holding a bazooka can do some stabilization and fire at an exact moment the target is in crosshairs.
Making a bazooka much more like a gun on a sailing ship, able to time their fire with the roll of the ship, while a howitzer would be more akin to a mortar on an 19th century bomb ketch, where precision of aiming, powder needed for the shot and timing of the fuse are arrived at by trial and error. (I am reading through the Hornblower books for the umpteenth time, so Napoleonic sea warfare is fresh in my mind.)
