It is important to consider the context of the words you reference. The scene has just opened upon Shylock and Bassanio, who is approaching Shylock for a bond on Antonio's good credit. Shylock gives the impression that he is considering making the loan, but before making any commitment, he pauses, building up suspense and anxiety in Bassanio, who finally says,
May you stead me? Will you pleasure me? / Shall I know your answer?
In fact, Bassanio is so roiled that he takes a statement as a question:
Shylock: Antonio is a good man.
Bassanio: Have you heard any imputation to the contrary?
Then, in a circuitous fashion, Shylock muses on the specific form that Antonio's wealth takes. He makes it clear that "good" for him is synonymous with "able to pay when the bond comes to term." The term "sufficient" gains its ominous tone from the uncertain state of Antonio's wealth, which takes the form of trade goods currently being transported between ports. Shylock ponders the number of ways these goods can be lost:
But ships are boards, sailors but men; there be land-rats and water-rats, water thieves and land-thieves, I mean pirates, and then there is the peril of waters, winds, and rocks.
After cataloging this potential pit-falls, Shylock then confirms the bond:
The man is notwithstanding sufficient.
The movement of his speech from affirmation, to measured skepticism, to affirmation on uncertain credit suggests that Shylock is rendering this bond for reasons other than benign charity. The ominous tone is a result of the uncertainty of Antonio's wealth being converted from trade goods into currency.