We definitely don't want to significantly increase the number of ports you can book passage to, and as a result we don't want to increase the number of ships you can have at one time. However, we would very much like to increase your ability to store additional ships. Our current thinking is to set up a 'dry dock' in one particular port (maybe the capital, maybe any port you've built a warehouse in, maybe other), where you can put ships 'in storage'. You can store a much larger number of ships there, but their cargo holds must be empty, so we don't give you infinite cargo storage space. If you have an open ship slot, you can take one of those ships out of storage, and then use it normally.
Does that sound like it would meet you needs?