You should be able to have each of the perks as you purchase them otherwise there is little reason to keep playing the game as you do not have the opportunity to earn enough experience to round out your character for higher difficulties.
Beat the game in one setting you may want to consider different difficulty levels. Overall a very fun game. After a certain point trade became irrelevant because I could make more money simply sinking enemy ships so as a consequence the size of my cargo did not seem to matter.
What really annoys me is how difficult the first battle is which makes getting the achievement for not loosing a single fight almost impossible to get.