as an added bonus, investment in a port increases your country's relationship with the particular port. If your country's investments are high enough, the port may even decide to ally itself to your country, making good use of those tax free permits
for pirates, investing in a port reduces the port's loyalty to every country. You can use this to create a safe haven for your pirating activities by "buying off" some key ports.
Do remember, though that investing in a port that is allied with another country would result in a negative effect in your relationship with that country. (and investing enough to "buy off" a port usually nets a good increase in your fame in trading, so you'll probably want to do this often when playing Ali)