You can purchase most traits any time, only a few have a prerequisite of another lower trait. There are a few things in the ship 'upgrades' that don't make a lot of sense, but I imagine they will get better over time or at least be moddable.
Now as far as cannons go, I have a better idea in mind for HoO, just have to get the ship entity further along before I can work on that. Now the upgraded cannons make a tactical difference when you are running smaller boats into battles against larger ones. It just doesn't do a lot of good when you are in the largest ship and already have big guns and a lot of them. I don't know if you noticed, but the cannons reloaded at different speeds due to their size. You can see the higher decks reload much faster than the lower deck, so there is some drawback to the larger gun sizes. Also remember that my character is a much higher level than a starting one, so I have leveled up the cannon abilities pretty high and have reduced reloading speed as much as possible.
In all though, it is fun to play, easy to learn, and hard to master. All traits I like in a game.