Correct, these changes are all server side, but they require significant testing.
There are some server side changes we can make pretty trivially, provide a single number in an override file and restart the servers. We don't like doing that, however, because it's not very stable and very hard to maintain. Obviously for critical situations we will do it, but it's something we try to avoid unless there's a real crisis.
There will be more Open Sea spawn revisions in 1.4, and, likely, in 1.5 as well. While we can, and do, test the functionality of these changes quite thoroughly, it is very difficult to test the actual impact of the changes on live gameplay. I can, and do, sit outside a port on an internal test server and kill NPCs to test the rate of incoming ships, however without 800 other players in the world killing some of those ships on the way, it's very hard to predict how many ships you'll actually see.
While I am reducing the number of Evil Pirate Gangs that each port calls for, you will still see a large number of them at any given port. This is particularly true because Evil Pirate Gangs generally spawn much closer to their destination port than other ship types.
I know that many players avoid killing NPC merchants to preserve their faction with that nation, and while I respect that, I want to make that a difficult choice. I want you to actually give up something by choosing to maintain your standing with a faction you're at war with. While I am certainly not trying to create a situation where those are the only NPC ships available to kill on the Open Sea, I do want players who are willing to take the war to their enemies to gain an advantage from it. Personally, I tend to level on the Open Sea (more experience per kill, and I get to fight higher level ships), so I am sympathetic to your concerns.
Finally, I wanted to note a couple of things for your information:
-Ports change the composition of the ships they call for when they change states, but ships already on the way do not change. This makes it entirely possible that you will see ships of a third party nation show up to a port that has just moved into Unrest, or that has moved back and forth between Unrest and normal.
-Ports call for many more ships during the Unrest phase (5000 unrest to port flip). This is the phase where I feel it is most important for players to have access to ships of the appropriate nations.