Increasing the number of companion ships will make pirating and privateering obscenely profitable. I can already make a lot of money by raiding a convoy, picking the three most profitable looking ships, capturing them, and heading for port. It's going to get silly if I can bag the whole convoy...
Increasing the number of officers is likely to cause trouble at bottlenecks. I ran into a similar problem while developing the "Hornblower" extension. Originally I wanted all the riflemen to follow you back to the ship, but the narrow passage leading to the beach is already difficult to pass if you have just the three normal officers, and impossible if the extra riflemen are there as well. So I arranged for them to make their own way back to the ship (i.e. they disappear before you get to the shore). More than three officers means some places are going to be impassable, especially if you don't enable sidestep in "InternalSettings.h".
Increasing the number of officers is likely to cause trouble at bottlenecks. I ran into a similar problem while developing the "Hornblower" extension. Originally I wanted all the riflemen to follow you back to the ship, but the narrow passage leading to the beach is already difficult to pass if you have just the three normal officers, and impossible if the extra riflemen are there as well. So I arranged for them to make their own way back to the ship (i.e. they disappear before you get to the shore). More than three officers means some places are going to be impassable, especially if you don't enable sidestep in "InternalSettings.h".