Ah, hypocrisy: the gift that keeps giving. Well, if you're on Malta, anyway. Generally speaking, hypocrisy is claiming you have one set of moral standards and then acting according to a different set of rules. Sounds bad, right? Sure. But remember that The Jew of Malta is presided over by Machiavelli, a guy who thought that hypocrisy was fine and dandy as long as it kept you in power. For a politician like Ferneze, hypocrisy lets you have your gold and bathe in it too: you sound good, because you openly espouse Christian morals, but you also get the luxury of doing really immoral things.
Power matters more than morality in this play, so hypocrisy is less a personal sin and more of a useful tool—you get all the advantages of professing morality while getting away with really immoral behavior.
Barabas claims that "A counterfeit profession is better/Than unseen hypocrisy (1.2.289-290), but ultimately his own "counterfeit profession" falls flat before Ferneze's "unseen hypocrisy."