@Jefromi is correct, there are card pieces that you can use to cover over the ports printed on the sea frame. In this image you can see the port pieces covering the printed ones. They are used to randomise the ports, in a similar way to randomising the tiles. Note that they only change what type of port it is, and not its location.
Seafarers of Catan also comes with additional port pieces, but they are used in a different way specific to that expansion.
To answer your comment, there is a specific reason that the ports are arranged as they are in the board game. This is to do with balance of the game: if they are arranged differently then you could get ports too close together, which makes that area of the board much more powerful than it otherwise would be. To avoid this, each port needs to be at least two hex edges away from its nearest neighbour. As the board only has 30 outside edges, with nine ports this only leaves three leftover edges, so the possible variations are all very similar to each other if you try to space the ports out evenly. As to why there are nine ports, not ten, I don't know, but I expect the game designer tried the game with different variations and found nine to make a better game than ten.
To quote Andrew Flynn's answer:
The reason I chose not to force harbors positions even after the new version is I found that it was possible to create better and more variable board setups if I didn't add the constraint of fixed harbors.
While I haven't played Andrew's game, I would be surprised if it allows ports to be too close together, and so while the exact locations may be different, the board will look similar and the overall balance of the game won't be affected. (The screenshots I've seen seem to support this.)
As an aside, the Seafarers of Catan introduces many scenarios with different port locations, but the ports are still carefully placed, and the "variable setup" rules suggest you don't move them (although you can shuffle them up, as usual). Again, this shows that the placement of ports is very important to the balance of the game, and shouldn't be messed with too much to avoid breaking it.